Alignments for a candidate for rocA in Ochrobactrum thiophenivorans DSM 7216

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Ochrobactrum thiophenivorans DSM 7216

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_094508021.1 CEV31_RS15250 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

Query= reanno::azobra:AZOBR_RS23695
         (1235 letters)



>NCBI__GCF_002252445.1:WP_094508021.1
          Length = 1227

 Score = 1574 bits (4076), Expect = 0.0
 Identities = 822/1222 (67%), Positives = 951/1222 (77%), Gaps = 13/1222 (1%)

Query: 18   FADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAATARKLITALRA 77
            F +FAPPIR  T LR AIT AYRRPE EC+  + +QA+LP         TARKLI ALRA
Sbjct: 13   FQNFAPPIRVQTPLRKAITDAYRRPEAECVTAIVQQATLPEETAKQVRETARKLIEALRA 72

Query: 78   KPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAGGDWQAHLGKG 137
            K +G GVEGL+HEYSLSSQEG+ALMCLAEALLRIPD ATRDALIRDKI+ GDW++H+G G
Sbjct: 73   KHKGTGVEGLVHEYSLSSQEGVALMCLAEALLRIPDMATRDALIRDKISNGDWKSHVGGG 132

Query: 138  GSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGVDFAMRMMGEQFVT 197
             S+FVNAATWGL++TGKLT+   +  LS+ALTRLIAR GEP+IRRGVD AMRMMGEQFVT
Sbjct: 133  RSLFVNAATWGLVVTGKLTNTVNDSGLSAALTRLIARCGEPVIRRGVDMAMRMMGEQFVT 192

Query: 198  GQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAIGTASAGRGVY 257
            G+TI EAL  A+++E  GFRYSYDMLGEAA TA DA RYY DY  AIHAIG ASAGRG+Y
Sbjct: 193  GETIDEALKRAKSLEERGFRYSYDMLGEAATTAADAERYYKDYETAIHAIGRASAGRGIY 252

Query: 258  EGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDAEEADRLELSL 317
            +GPGISIKLSA+HPRY RAQ++RVM ELLP+VK LA L+K Y+IGLNIDAEEADRLELSL
Sbjct: 253  DGPGISIKLSALHPRYVRAQSERVMSELLPKVKELAALSKQYNIGLNIDAEEADRLELSL 312

Query: 318  DLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIRLVKGAYWDSE 377
            DL++SL  DPDLA W GIGFVVQAYGKRCP+V+DF+IDLARR+  R+M+RLVKGAYWD+E
Sbjct: 313  DLLQSLIEDPDLADWEGIGFVVQAYGKRCPFVLDFIIDLARRNNRRVMVRLVKGAYWDAE 372

Query: 378  IKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQTLATIYEMAGS 437
            IKRAQ+DGL DFPVYTRKV+TDVSY+ACA KLL A + +FPQFATHNAQTLATIY +AG 
Sbjct: 373  IKRAQVDGLEDFPVYTRKVHTDVSYIACAAKLLGARDVIFPQFATHNAQTLATIYHLAGP 432

Query: 438  DFQVGKYEFQCLHGMGEPLYKEVVGPLK--RPCRIYAPVGTHETLLAYLVRRLLENGANS 495
            DF+ G YEFQCLHGMGEPLY EVVG  K  RP RIYAPVGTHETLLAYLVRRLLENGANS
Sbjct: 433  DFKTGSYEFQCLHGMGEPLYDEVVGASKLGRPARIYAPVGTHETLLAYLVRRLLENGANS 492

Query: 496  SFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERANSAGIDLSDET 555
            SFVNRI D +V VDEL+ADP  V R++A  GA H  I+LP  LY   R NS G DLS+E 
Sbjct: 493  SFVNRIGDKSVSVDELIADPAEVVRSMAVVGARHDQISLPEGLYG-IRKNSVGFDLSNEE 551

Query: 556  ELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVTEASEALVAEAF 615
            +LA LS  L A+A   WTA P +   +  G+++PV NP D  DVVG+VTE +   VA+A 
Sbjct: 552  QLAELSETLKANATRAWTAEPQVVGSKVKGESRPVLNPGDHSDVVGTVTEIAADDVAQAM 611

Query: 616  GHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAIAEVREAID 675
              A  A ++W+   P +RAA L RAAD MQ  M  LLGLI+REAGKS+PNAIAEVREAID
Sbjct: 612  KAAEKAVASWSHVLPADRAACLDRAADIMQREMAELLGLIMREAGKSMPNAIAEVREAID 671

Query: 676  FLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVLAKPAEETP 735
            FLRYY  Q R R     H+PLGP+VCISPWNFPLAIF+GQIAAAL AGNPVLAKPAEETP
Sbjct: 672  FLRYYAEQTR-RTLGVAHKPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETP 730

Query: 736  LIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGSTEVARLIQRQLAG 795
            LIAA+ VRILH AGIPA ALQLLPG G +GAALV  +   GVMFTGSTEVARLIQ QLA 
Sbjct: 731  LIAAQGVRILHEAGIPADALQLLPGDGRIGAALVAAQETCGVMFTGSTEVARLIQAQLAS 790

Query: 796  RLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRILCLQEDV 855
            RLLP+G PIPLIAETGGQNAMIVDSSALAEQVV DVI SAFDSAGQRCSALR+LCLQEDV
Sbjct: 791  RLLPNGKPIPLIAETGGQNAMIVDSSALAEQVVFDVIGSAFDSAGQRCSALRVLCLQEDV 850

Query: 856  ADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRNVEFLPLPA 915
            ADR L MLKGA++EL IG  D+L VD+G VI+ EA+  I  H++ MR  GR VE LPL  
Sbjct: 851  ADRILTMLKGALKELSIGRTDKLKVDIGAVITAEAKDIIEKHVQTMRDMGRKVEQLPLGP 910

Query: 916  ETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSINATGYGLTFGLHT 975
            ET  GTF+APT++EI  + +L+REVFGPVLHVVR+ R+D+D+L+D INATGYGLTFGLHT
Sbjct: 911  ETGKGTFVAPTIVEIDSLRDLKREVFGPVLHVVRYKRNDMDSLIDDINATGYGLTFGLHT 970

Query: 976  RIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGGPLYLSRLLSRRP 1035
            R+D TI  V  RI  GN+Y+NRN IGA+VGVQPFGG GLSGTGPKAGGPLYL RL+   P
Sbjct: 971  RLDETIAHVADRIRVGNIYINRNVIGAIVGVQPFGGRGLSGTGPKAGGPLYLGRLVETAP 1030

Query: 1036 KGWLEFRGPDAARAAGL-AYGEWLRAKGFT--AEASRCAGYVARSAIGGGAELNGPVGER 1092
               +  R         L  + +WL  +G    A+A+R  G  + SA+G   EL GPVGER
Sbjct: 1031 ---IPPRMASVHSDPALNDFAKWLGNRGMNELAQAARETG--SASALGLNIELPGPVGER 1085

Query: 1093 NLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLPPALAARVRT 1152
            NLY LH RGR+LL PQT +GL  QL A LATGN A +D    L  +L+GLP ++AARV  
Sbjct: 1086 NLYALHARGRILLAPQTESGLYRQLTAALATGNEAIIDEASGLRNVLKGLPSSVAARVVW 1145

Query: 1153 TADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGRGEGYDLDLL 1212
            T DW+   P A  LVEG+ ER+  IN+++A LPGP++L QAAT+  LA    + Y L  L
Sbjct: 1146 TKDWQADAPFAGALVEGEGERLIDINKKLAALPGPLVLTQAATSAQLAQ-NADCYCLSWL 1204

Query: 1213 LNERSVSVNTAAAGGNASLVAM 1234
            L E S S+NT AAGGNASL+A+
Sbjct: 1205 LEEVSTSINTTAAGGNASLMAI 1226


Lambda     K      H
   0.319    0.136    0.396 

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: 3574
Number of extensions: 150
Number of successful extensions: 6
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: 1235
Length of database: 1227
Length adjustment: 47
Effective length of query: 1188
Effective length of database: 1180
Effective search space:  1401840
Effective search space used:  1401840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (27.3 bits)

Align candidate WP_094508021.1 CEV31_RS15250 (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.1013585.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.1e-223  726.7   0.9   8.9e-223  726.2   0.9    1.2  1  NCBI__GCF_002252445.1:WP_094508021.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002252445.1:WP_094508021.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  726.2   0.9  8.9e-223  8.9e-223       2     497 ..     535    1027 ..     534    1030 .. 0.98

  Alignments for each domain:
  == domain 1  score: 726.2 bits;  conditional E-value: 8.9e-223
                             TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsead 72  
                                            lyg  rkns G dl+ne++l++l+e l++ a++ + a p v   +k +ge +pv np d+ d+vG+v+e  
  NCBI__GCF_002252445.1:WP_094508021.1  535 LYGI-RKNSVGFDLSNEEQLAELSETLKANATRAWTAEPQV-VGSKVKGESRPVLNPGDHSDVVGTVTEIA 603 
                                            6887.**********************************99.4567789********************** PP

                             TIGR01238   73 aaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflr 143 
                                            a++v +a+++a +a+a ws + +++raa+l+r+ad+++++m el++l++reaGk++ naiaevrea+dflr
  NCBI__GCF_002252445.1:WP_094508021.1  604 ADDVAQAMKAAEKAVASWSHVLPADRAACLDRAADIMQREMAELLGLIMREAGKSMPNAIAEVREAIDFLR 674 
                                            *********************************************************************** PP

                             TIGR01238  144 yyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaG 214 
                                            yya+q + +l+   +k+lG++vcispwnfplaiftGqiaaal+aGn v+akpae+t+liaa++v +l+eaG
  NCBI__GCF_002252445.1:WP_094508021.1  675 YYAEQTRRTLGVA-HKPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETPLIAAQGVRILHEAG 744 
                                            **********988.********************************************************* PP

                             TIGR01238  215 vpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivd 282 
                                            +pa ++qllpG G  +Gaal + +   Gv+ftGstevarli+ +la+r  ++   +pliaetGGqnamivd
  NCBI__GCF_002252445.1:WP_094508021.1  745 IPADALQLLPGDGR-IGAALVAAQETCGVMFTGSTEVARLIQAQLASRLLPNgkpIPLIAETGGQNAMIVD 814 
                                            *************9.*********************************8765555**************** PP

                             TIGR01238  283 stalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaea 353 
                                            s+alaeqvv dv+ safdsaGqrcsalrvlc+qedvadr+lt++kGa++el +g+  +l+ d+G vi aea
  NCBI__GCF_002252445.1:WP_094508021.1  815 SSALAEQVVFDVIGSAFDSAGQRCSALRVLCLQEDVADRILTMLKGALKELSIGRTDKLKVDIGAVITAEA 885 
                                            *********************************************************************** PP

                             TIGR01238  354 kqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvv 424 
                                            k+ +++h++ m+++++kv q+ l    e+ kgtfvapt++e+d+l +lk+evfGpvlhvvryk++++d+++
  NCBI__GCF_002252445.1:WP_094508021.1  886 KDIIEKHVQTMRDMGRKVEQLPLGP--ETGKGTFVAPTIVEIDSLRDLKREVFGPVLHVVRYKRNDMDSLI 954 
                                            ***********************99..99****************************************** PP

                             TIGR01238  425 dkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrl 495 
                                            d ina+Gyglt+G+h+r +et++++ +r++vGn+y+nrn++Ga+vGvqpfGG+GlsGtGpkaGGplyl rl
  NCBI__GCF_002252445.1:WP_094508021.1  955 DDINATGYGLTFGLHTRLDETIAHVADRIRVGNIYINRNVIGAIVGVQPFGGRGLSGTGPKAGGPLYLGRL 1025
                                            **********************************************************************9 PP

                             TIGR01238  496 tr 497 
                                            ++
  NCBI__GCF_002252445.1:WP_094508021.1 1026 VE 1027
                                            87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1227 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 47.50
//
[ok]

This GapMind analysis is from Sep 24 2021. 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