Alignments for a candidate for rocA in Azohydromonas australica DSM 1124

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Azohydromonas australica DSM 1124

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_051243110.1 H537_RS44845 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

Query= reanno::Cup4G11:RR42_RS20125
         (1333 letters)



>NCBI__GCF_000430725.1:WP_051243110.1
          Length = 1249

 Score = 1447 bits (3745), Expect = 0.0
 Identities = 778/1259 (61%), Positives = 927/1259 (73%), Gaps = 19/1259 (1%)

Query: 81   PFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLEQARLPHQQAEAALAMARTLATRLR 140
            PFL+FA  + PQSVLR+AITAA RRPE E V +LLE ARLP  QA + LA+A +LA RLR
Sbjct: 4    PFLDFAGELLPQSVLRSAITAACRRPEPEAVAMLLESARLPPGQAVSVLALAASLARRLR 63

Query: 141  ERKVG--TGREGLVQGLIQEFSLSSQEGVALMCLAEALLRIPDKATRDALIRDKISGANW 198
            ER  G   GREGLVQGL++EFSL+SQEGVALMCLAEALLRIPD ATRDALIRDK+   +W
Sbjct: 64   ERGAGLTAGREGLVQGLMREFSLASQEGVALMCLAEALLRIPDDATRDALIRDKLGDGDW 123

Query: 199  QSHLGQSPSVFVNAATWGLLFTGKLVATH-TEAGLSKALTRIIGKGGEPLIRKGVDMAMR 257
             +HLG+S S+FVNAATWGLL  G++ AT   EAGL  AL+R++ + GEPL+RKGVD+AMR
Sbjct: 124  GAHLGRSGSLFVNAATWGLLLGGRMAATQQAEAGLGSALSRVLARSGEPLLRKGVDLAMR 183

Query: 258  LMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTEADAQRYLASYEQAINAIGQ 317
            L+GEQFV G+TI EALA ARK E++GF YS+DMLGEAA+T  DAQRYL++YE AI+A+G 
Sbjct: 184  LLGEQFVCGQTIGEALARARKRESQGFTYSFDMLGEAALTAEDAQRYLSAYEHAIHALGI 243

Query: 318  ASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLKSLTLLARQYDIGINIDAEE 377
            A  GR ++ GPGISIKLSALHPRY+R+QH RV+ ELY RL  L LLAR + IG++IDAEE
Sbjct: 244  ALAGRDLHAGPGISIKLSALHPRYTRSQHGRVMAELYPRLLQLALLARHHGIGLSIDAEE 303

Query: 378  ADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVIDYLIDLARRSRHRLMIRLV 437
            ADRLE+SLDLL+RLC E  LAGW+G+G  VQ YQKRCP V+D+ IDLARRSR RLM+RLV
Sbjct: 304  ADRLELSLDLLQRLCGEHMLAGWSGLGLAVQAYQKRCPHVLDFCIDLARRSRRRLMLRLV 363

Query: 438  KGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLLSVPDVIYPQFATHNAHTLA 497
            KGAYWDSEIKRAQ+DGLE Y VYTRK +TDV+Y+ACAR+LL+ PD +YPQFATHNAHT+A
Sbjct: 364  KGAYWDSEIKRAQIDGLEDYAVYTRKAHTDVAYLACARRLLAAPDAVYPQFATHNAHTVA 423

Query: 498  AIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGKFNRPCRIYAPVGTHETLLAYL 557
            AI  +AG  + PG+YEFQCLHGMGEPLY+ VV P  +G    PCRIYAPVGTHETLLAYL
Sbjct: 424  AIQHLAG-AWTPGRYEFQCLHGMGEPLYEMVVAPPIEGGLGLPCRIYAPVGTHETLLAYL 482

Query: 558  VRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMHADEGALGLPHPRIAQPRTLYG 617
            VRRLLENGANTSFVNRIAD +I ++ LV DPVA VE+    EG LGLPHP I  PR L+G
Sbjct: 483  VRRLLENGANTSFVNRIADASIPVEALVEDPVAQVERAARAEGTLGLPHPAIPLPRALFG 542

Query: 618  ESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLGTEAAAGEDVNQPAPVRNPSDQ 677
              R NSAGIDL+NEHRLASLS+ALL G  +A +AVPL+      G+    P PV NP+D+
Sbjct: 543  ALRPNSAGIDLANEHRLASLSAALLHGARQAWTAVPLVAGLPRPGD---LPQPVLNPADR 599

Query: 678  RDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAAALERAAELMEAQMQSLMGIIV 737
             D VG V EA   E+E AL AA    P W ATP   RAA LER A+ +E Q+Q+L+G+IV
Sbjct: 600  SDRVGTVREARADEMEDALSAAAAVQPAWGATPPAERAALLERGADALEDQLQTLVGLIV 659

Query: 738  REAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRPLGPVVCISPWNFPLAIFTGQV 797
            REAGKT   A+ EVREAVD LRY A Q R    + + RPLGPV CISPWNFPLAIFTGQ+
Sbjct: 660  REAGKTVPAAVGEVREAVDALRYAALQARTALDAGS-RPLGPVACISPWNFPLAIFTGQL 718

Query: 798  AAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLLPGRGETVGAALVGDARVK 857
            AAALAAGN V+AKPA QTPL+AA+AVRLL  AGVP   +QLLPG GE+VG  L  DARV+
Sbjct: 719  AAALAAGNAVVAKPARQTPLVAAEAVRLLHAAGVPGAVLQLLPGPGESVGLRLARDARVR 778

Query: 858  GVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQNAMIVDSSALAEQVVGDVVNSA 917
            GV+FTGST VAR LQ  +A RLDA G P  L+AETGG NA+I DSSALAEQ+V DV+ SA
Sbjct: 779  GVLFTGSTAVARRLQAELALRLDARGVPPLLVAETGGLNALIADSSALAEQLVPDVLASA 838

Query: 918  FDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGNPDRLSTDVGPVIDEEARGNIV 977
            FDSAGQRCSALRVLCLQ+E+A+ VL ML+GA+ EL +G PD L+TDVGPVID+ AR  + 
Sbjct: 839  FDSAGQRCSALRVLCLQQEIAEPVLRMLQGALAELCVGRPDALATDVGPVIDDTARDTVE 898

Query: 978  RHIDAMRAKGRRVHQADPNGALSAACRNGTFVSPTLIELDSIEELQREVFGPVLHVVRYP 1037
            +H+  M+A G RV +   +  L     +G+FV+PT++EL+S+ +L  EVFGPVLHV+R+ 
Sbjct: 899  KHVLHMQALGLRVTRQPLSEELR---EHGSFVAPTVVELESLSQLPGEVFGPVLHVLRWR 955

Query: 1038 RAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEVGNLYVNRNIVGAVVGVQPFGG 1097
            R  LD LL +I  TGY LT+G+HTRIDETI  +  RA  GN YVNRN++GAVVGVQPFGG
Sbjct: 956  RGELDGLLQRIEATGYALTLGLHTRIDETIALVTARARAGNQYVNRNMIGAVVGVQPFGG 1015

Query: 1098 EGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRASDTVGGADETGPVRRTLTETLATLKE 1157
            EGLSGTGPKAGGPL + RL   C   A A +   +     A             L  L+ 
Sbjct: 1016 EGLSGTGPKAGGPLLVRRL---CERHAPALLAIGTPVAAVAPSGNGGGEPRLPALRVLRG 1072

Query: 1158 WAQRESAALPGLVAACERFAAASAAGLSVTLPGPTGERNTYTLLPRAAVLCLAQQETDLA 1217
            W Q        LVAAC+   A S AGL V LPGPTGERN Y LLPR  VLC A    DL 
Sbjct: 1073 WLQEALPEDAALVAACDALLAQSPAGLDVLLPGPTGERNRYALLPRRRVLCQAGDRGDLL 1132

Query: 1218 VQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRVRLVADWSAGDTGFDAVLHHGDSDQ 1277
              LA VLA G + +W +S  ARAL A LP  V+ RV+L A+    D   D         +
Sbjct: 1133 FLLALVLATGGRVLWADSAAARALHAALPAVVRERVKLSANPLGED--IDLAAAQDAPGR 1190

Query: 1278 LRAVCEQLATRPGPIISVQGLAHGEPNIAI---ERLLIERSLSVNTAAAGGNASLMTIG 1333
            +  +   L+ R GPI+ +   A GE + A+   ERL++ERSL VNTAAAGGNA LM +G
Sbjct: 1191 VLELSLALSQRDGPIVPLVACAKGERDPALLPPERLMVERSLCVNTAAAGGNAGLMAMG 1249


Lambda     K      H
   0.318    0.133    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 4010
Number of extensions: 186
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1333
Length of database: 1249
Length adjustment: 48
Effective length of query: 1285
Effective length of database: 1201
Effective search space:  1543285
Effective search space used:  1543285
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (27.3 bits)

Align candidate WP_051243110.1 H537_RS44845 (trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01238.hmm
# target sequence database:        /tmp/gapView.3919516.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.8e-207  673.8   0.2     9e-207  673.4   0.2    1.1  1  NCBI__GCF_000430725.1:WP_051243110.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000430725.1:WP_051243110.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  673.4   0.2    9e-207    9e-207       2     497 ..     540    1036 ..     539    1039 .. 0.98

  Alignments for each domain:
  == domain 1  score: 673.4 bits;  conditional E-value: 9e-207
                             TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsead 72  
                                            l+g  r ns+G+dlane++l+sl++ ll+ a + + a+p+v++ ++  +  qpv npadr d vG+v+ea 
  NCBI__GCF_000430725.1:WP_051243110.1  540 LFGALRPNSAGIDLANEHRLASLSAALLHGARQAWTAVPLVAGLPRPGDLPQPVLNPADRSDRVGTVREAR 610 
                                            8999******************************************************************* PP

                             TIGR01238   73 aaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflr 143 
                                            a+e+++a+++a a  + w at+++eraa ler ad le ++ +lv+l+vreaGkt+  a+ evreavd lr
  NCBI__GCF_000430725.1:WP_051243110.1  611 ADEMEDALSAAAAVQPAWGATPPAERAALLERGADALEDQLQTLVGLIVREAGKTVPAAVGEVREAVDALR 681 
                                            *********************************************************************** PP

                             TIGR01238  144 yyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaG 214 
                                            y a q++  ld    ++lG+v cispwnfplaiftGq+aaalaaGn+v+akpa qt+l+aa+av ll+ aG
  NCBI__GCF_000430725.1:WP_051243110.1  682 YAALQARTALDAG-SRPLGPVACISPWNFPLAIFTGQLAAALAAGNAVVAKPARQTPLVAAEAVRLLHAAG 751 
                                            **********998.8******************************************************** PP

                             TIGR01238  215 vpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivd 282 
                                            vp +v+qllpG Ge+vG  l+ d+r++Gv+ftGst+var+++ +la r da+     l+aetGG na+i d
  NCBI__GCF_000430725.1:WP_051243110.1  752 VPGAVLQLLPGPGESVGLRLARDARVRGVLFTGSTAVARRLQAELALRLDARgvpPLLVAETGGLNALIAD 822 
                                            **************************************************98744469************* PP

                             TIGR01238  283 stalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaea 353 
                                            s+alaeq+v dvlasafdsaGqrcsalrvlc+q+++a+ vl +++Ga+ el vg+p  l tdvGpvid+ a
  NCBI__GCF_000430725.1:WP_051243110.1  823 SSALAEQLVPDVLASAFDSAGQRCSALRVLCLQQEIAEPVLRMLQGALAELCVGRPDALATDVGPVIDDTA 893 
                                            *********************************************************************** PP

                             TIGR01238  354 kqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvv 424 
                                            ++ +++h+ +m+a + +v++  l +    e+g+fvapt++el++l++l  evfGpvlhv+r+++ eld ++
  NCBI__GCF_000430725.1:WP_051243110.1  894 RDTVEKHVLHMQALGLRVTRQPLSE-ELREHGSFVAPTVVELESLSQLPGEVFGPVLHVLRWRRGELDGLL 963 
                                            ***************9999888887.4679***************************************** PP

                             TIGR01238  425 dkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrl 495 
                                            ++i+a+Gy+ltlG+h+ri+et++ ++ ra++Gn yvnrn++GavvGvqpfGGeGlsGtGpkaGGpl + rl
  NCBI__GCF_000430725.1:WP_051243110.1  964 QRIEATGYALTLGLHTRIDETIALVTARARAGNQYVNRNMIGAVVGVQPFGGEGLSGTGPKAGGPLLVRRL 1034
                                            *******************************************************************9999 PP

                             TIGR01238  496 tr 497 
                                             +
  NCBI__GCF_000430725.1:WP_051243110.1 1035 CE 1036
                                            75 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1249 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 62.16
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources