Alignments for a candidate for putA in Steroidobacter denitrificans DSM 18526

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Steroidobacter denitrificans DSM 18526

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_083536806.1 ACG33_RS11175 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::SB2B:6938573
         (1058 letters)



>NCBI__GCF_001579945.1:WP_083536806.1
          Length = 1099

 Score = 1001 bits (2587), Expect = 0.0
 Identities = 547/1066 (51%), Positives = 697/1066 (65%), Gaps = 33/1066 (3%)

Query: 16   NLDELFSLISQNYIVDEEAYLKELIALVPSSDEEIARITSRAHDLVAKVRQYEKKGLMVG 75
            NL  L +        +E   +  L+A V  S  +  R+ ++A   V++ R   +KG    
Sbjct: 41   NLAALRAAFRSALYTEETQAVNALLAAVQLSQADRTRMVAQASRFVSRTRA--RKGERGV 98

Query: 76   IDAFLQQYSLETQEGIILMCLAEALLRIPDAETADALIADKLSGAKWDEHMSKSDSVLVN 135
            ++ FLQ+Y L + EGI L+CLAEALLR+PDA+TAD LIA+KL    W  H S+SDS +VN
Sbjct: 99   LEVFLQEYGLSSDEGIALLCLAEALLRVPDAQTADNLIAEKLRSGAWSAHRSQSDSTVVN 158

Query: 136  ASTWGLMLTGKIVQLDKNLDGTPSNLLSRLVNRLGEPVIRQAMYAAMKIMGKQFVLGRTI 195
            A+T  LML+  IV LD  L G  + LL  LVNRLGEPV+R A   AMKIMG +FVLGRTI
Sbjct: 159  AATRALMLSSGIVALDTRLSGQDNGLLRSLVNRLGEPVVRAATRQAMKIMGNEFVLGRTI 218

Query: 196  EEGLKNAAEKRKLGYTHSYDMLGEAALTMKDADKYYRDYANAIQALGTAKFDESEAPRPT 255
            EE L  A +   +    S+DMLGE A T  DA +Y+  Y+ +I     A   +  A    
Sbjct: 219  EEALDKAQQTHCVA---SFDMLGEGARTAADAQRYFESYSRSIDVTAAAARGDVYAAHG- 274

Query: 256  ISIKLSALHPRYEVANEDRVMTELYATLIKLIEQARSLNVGIQIDAEEVDRLELSLKLFK 315
            +S+KLSALHPRY+ AN+ RV+ E+   L +L  QA +  + + IDAEE  RL+LSL+  +
Sbjct: 275  VSVKLSALHPRYDYANQTRVLREMLPRLRRLALQACAGGISMTIDAEEAARLDLSLEFIE 334

Query: 316  KLYQSDAAKGWGLLGIVVQAYSKRALPVLMWLTRLAKEQGDEIPLRLVKGAYWDSELKWA 375
             L +      W  LG+ VQ YSKRA  +L WL  L ++ G    LRLVKGAYWD+E+K A
Sbjct: 335  ALARDRELAHWQGLGLAVQCYSKRAPALLDWLIALGRDTGRRFMLRLVKGAYWDTEIKRA 394

Query: 376  QQAGEAGYPLFTRKAATDVSYLACARYLLSEATRGVIYPQFASHNAQTVAAITAMVGDRK 435
            Q+ G AGYP+FTRK +TD+ YLACAR  L+     V YPQFA+HNA T+A +  M G+R+
Sbjct: 395  QELGVAGYPVFTRKMSTDLCYLACARKALAHPE--VFYPQFATHNAHTIAGVLQMAGERR 452

Query: 436  -FEFQRLHGMGQELYDTVLAEAA-VPTVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHK 493
             FEFQRLHGMG+ LY  V  +   +P VR+YAP+GAH+DLL YLVRRLLENGAN+SFV++
Sbjct: 453  DFEFQRLHGMGELLYSAVRDQVPDLPQVRVYAPVGAHRDLLAYLVRRLLENGANSSFVNR 512

Query: 494  LVDPKTPIESLVTHPLKTLQGYKTLANNKIVKPADIF-GAE------------------- 533
             +D +T IE LV  P+  +    +L N KI  P  ++ GA                    
Sbjct: 513  FMDERTAIERLVEDPVARILSLPSLPNPKIPLPCALYEGASAEAPCGQDINAENPFLSDN 572

Query: 534  ---RKNSKGLNMNIISESEPFFAALEKFKDTQWSAGPLVNGETLSGEVRDVVSPYNTTLK 590
               R+NS GL++N   E+    A L   K+ QW+AGP+V+G         + +P + T  
Sbjct: 573  LSTRRNSTGLDLNDPQETAALLAKLGALKNRQWAAGPIVSGAVTGRGRLAITNPADHTDI 632

Query: 591  VGQVAFANEATIEQAIAGADKAFASWCRTPVETRANALQKLADLLEENREELIALCTREA 650
            VG V  A  A +++A+  A   +A+W     E RA  L++ AD LE  RE  ++L  REA
Sbjct: 633  VGHVWDATSADLDRALDAAVSNYAAWDAQGAEARAAVLERAADALEAGRERFLSLLVREA 692

Query: 651  GKSIQDGIDEVREAVDFCRYYAVQAKKMMSKPELLPGPTGELNELFLQGRGVFVCISPWN 710
            GK++ D + E REAVDFCRYYA QA+       LLPGPTGE N   L GRG FVCISPWN
Sbjct: 693  GKTVDDALAECREAVDFCRYYAQQARCRFGAAHLLPGPTGEQNLYSLHGRGAFVCISPWN 752

Query: 711  FPLAIFLGQVAAALATGNTVIAKPAEQTCLIGFRAVQLAHEAGIPKDVLQFLPGTGAVVG 770
            FPLAIFLGQV AALA GN V+AKPAEQT LI   A++L H AG+P DVL  LPGTG +VG
Sbjct: 753  FPLAIFLGQVTAALAAGNAVLAKPAEQTPLIAAEAIELLHRAGVPYDVLHLLPGTGEMVG 812

Query: 771  AKLTSDERIGGVCFTGSTTTAKVINRALAGRDGAIIPLIAETGGQNAMVVDSTSQPEQVV 830
            A L +DERI G   TGST TAK+I + LA R GAIIPLIAETGGQNAM VDST+ PEQVV
Sbjct: 813  AALVADERIAGAALTGSTATAKLIAKTLAARRGAIIPLIAETGGQNAMFVDSTALPEQVV 872

Query: 831  NDVVSSAFTSAGQRCSALRVLYLQEDIAERVLDVLKGAMDELTLGNPGSVKTDVGPVIDA 890
            +DVV SAF SAGQRCSALRVLYLQ+++A+ ++++L GAMDEL++G+PG + TDVGPVID 
Sbjct: 873  DDVVRSAFHSAGQRCSALRVLYLQDEVADGIIEMLTGAMDELSVGDPGLLSTDVGPVIDE 932

Query: 891  AAKANLNAHIDHIKQVGRLIHQLSLPEGTENGHFVAPTAVEIDSIKVLTKENFGPILHVV 950
             A+  L AH++ ++  GRL+H   L E    G FVAP   EIDSI+ L +E+FGP+LHVV
Sbjct: 933  PARKALLAHVEALQAEGRLLHVSRLGEACARGTFVAPHLFEIDSIRRLEQEHFGPLLHVV 992

Query: 951  RYKAAGLQKVIDDINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQP 1010
            R++   L+K +  + +TGFGLTLG+H+R E  +  + D    GNVY+NRN IGAVVGVQP
Sbjct: 993  RFRLRDLEKHLAQLRATGFGLTLGVHTRIEAMSRRIFDASMAGNVYVNRNMIGAVVGVQP 1052

Query: 1011 FGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGD 1056
            FGG GLSGTGPKAGGP YL RF  E+  + N  A GGN TLL LGD
Sbjct: 1053 FGGHGLSGTGPKAGGPLYLPRFAAERVLSVNTAATGGNITLLRLGD 1098


Lambda     K      H
   0.317    0.134    0.380 

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: 2497
Number of extensions: 101
Number of successful extensions: 7
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: 1058
Length of database: 1099
Length adjustment: 46
Effective length of query: 1012
Effective length of database: 1053
Effective search space:  1065636
Effective search space used:  1065636
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: 58 (26.9 bits)

Align candidate WP_083536806.1 ACG33_RS11175 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA)
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.1503.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     7e-206  670.5   0.3   9.8e-206  670.0   0.3    1.1  1  lcl|NCBI__GCF_001579945.1:WP_083536806.1  ACG33_RS11175 bifunctional proli


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001579945.1:WP_083536806.1  ACG33_RS11175 bifunctional proline dehydrogenase/L-glutamate gamma-semialde
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  670.0   0.3  9.8e-206  9.8e-206       5     497 ..     574    1076 ..     572    1079 .. 0.98

  Alignments for each domain:
  == domain 1  score: 670.0 bits;  conditional E-value: 9.8e-206
                                 TIGR01238    5 egrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsea 71  
                                                ++r+ns+G+dl+  +e + l ++l +  ++++ a piv++     g    ++npad+ divG+v  a
  lcl|NCBI__GCF_001579945.1:WP_083536806.1  574 STRRNSTGLDLNDPQETAALLAKLGALKNRQWAAGPIVSGAVTGRGR-LAITNPADHTDIVGHVWDA 639 
                                                579***********************************777666665.57***************** PP

                                 TIGR01238   72 daaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevrea 138 
                                                  a+ ++a+d+av+++a w a  a+ raa+ler+ad le     +++llvreaGkt+++a+ae rea
  lcl|NCBI__GCF_001579945.1:WP_083536806.1  640 TSADLDRALDAAVSNYAAWDAQGAEARAAVLERAADALEAGRERFLSLLVREAGKTVDDALAECREA 706 
                                                ******************************************************************* PP

                                 TIGR01238  139 vdflryyakqvedvldeesaka.............lGavvcispwnfplaiftGqiaaalaaGntvi 192 
                                                vdf+ryya+q++  ++     +             +Ga+vcispwnfplaif+Gq++aalaaGn+v+
  lcl|NCBI__GCF_001579945.1:WP_083536806.1  707 VDFCRYYAQQARCRFGAAHLLPgptgeqnlyslhgRGAFVCISPWNFPLAIFLGQVTAALAAGNAVL 773 
                                                ***************999777799999**************************************** PP

                                 TIGR01238  193 akpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkal 259 
                                                akpaeqt+liaa+a+ell+ aGvp  v+ llpG Ge vGaal +deriaG ++tGst++a+li k+l
  lcl|NCBI__GCF_001579945.1:WP_083536806.1  774 AKPAEQTPLIAAEAIELLHRAGVPYDVLHLLPGTGEMVGAALVADERIAGAALTGSTATAKLIAKTL 840 
                                                ******************************************************************* PP

                                 TIGR01238  260 akredapvpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltli 326 
                                                a r  a +pliaetGGqnam vdstal+eqvv dv++saf saGqrcsalrvl++q++vad +++++
  lcl|NCBI__GCF_001579945.1:WP_083536806.1  841 AARRGAIIPLIAETGGQNAMFVDSTALPEQVVDDVVRSAFHSAGQRCSALRVLYLQDEVADGIIEML 907 
                                                ******************************************************************* PP

                                 TIGR01238  327 kGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlf 393 
                                                 Gamdel vg p++l tdvGpvid+ a++ llah+e+++a ++ ++  +l +  ++ +gtfvap lf
  lcl|NCBI__GCF_001579945.1:WP_083536806.1  908 TGAMDELSVGDPGLLSTDVGPVIDEPARKALLAHVEALQAEGRLLHVSRLGE--ACARGTFVAPHLF 972 
                                                *********************************************9999988..9************ PP

                                 TIGR01238  394 elddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyv 460 
                                                e+d++  l++e fGp+lhvvr++ ++l+k + ++ a+G+gltlGvh+rie   r+i +   +Gnvyv
  lcl|NCBI__GCF_001579945.1:WP_083536806.1  973 EIDSIRRLEQEHFGPLLHVVRFRLRDLEKHLAQLRATGFGLTLGVHTRIEAMSRRIFDASMAGNVYV 1039
                                                ******************************************************************* PP

                                 TIGR01238  461 nrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 
                                                nrn++GavvGvqpfGG+GlsGtGpkaGGplyl r+  
  lcl|NCBI__GCF_001579945.1:WP_083536806.1 1040 NRNMIGAVVGVQPFGGHGLSGTGPKAGGPLYLPRFAA 1076
                                                *********************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1099 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 14.05
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 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