Alignments for a candidate for pad-dh in Rhodobacter ovatus JA234

GapMind for catabolism of small carbon sources

Alignments for a candidate for pad-dh in Rhodobacter ovatus JA234

Align Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized)
to candidate WP_097030551.1 CRO07_RS10015 aldehyde dehydrogenase family protein

Query= SwissProt::O06837
         (502 letters)



>NCBI__GCF_900207575.1:WP_097030551.1
          Length = 772

 Score =  281 bits (718), Expect = 8e-80
 Identities = 188/462 (40%), Positives = 247/462 (53%), Gaps = 30/462 (6%)

Query: 27  GQWVNAQ---SDKTLNVYNPATGDTLTDVPDGDVEDVNAAVESAAATLQSDAWRRMPPSA 83
           G W++      D    + NPATG  L  V  G   DV+AAV SA        W +     
Sbjct: 34  GHWIDGAFGTPDTAFAIANPATGAVLAHVAQGTAADVDAAVTSARHA--QTEWAQRSGHD 91

Query: 84  RERILLRLADLLEAHGDELARLETLNNGKLLIYSKMMEVGASAQWLRYMAGWATKLTGST 143
           R R+L  LA L++ H   LA L+TL  GK L  S   ++   A+   Y AG A +L+G+ 
Sbjct: 92  RARVLYALARLVQKHSRLLALLQTLETGKPLRDSHDADLPLVARHFSYHAGLA-QLSGTE 150

Query: 144 LDLSLPLPPDVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAEET 203
                   P +        VP+GV AA+IPW+ PL M  WK+APALA GN VVLKP+ +T
Sbjct: 151 F-------PGL--------VPLGVCAAVIPWHAPLRMLAWKVAPALAAGNAVVLKPSRQT 195

Query: 204 PLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIGSAC 263
           PLTAL  A+L+ +AGLP G LNVVTG G T G ALV HP VAKVAF GST+VGR I  A 
Sbjct: 196 PLTALLFADLSRQAGLPPGVLNVVTGDGAT-GAALVAHPGVAKVAFAGSTKVGRQIRQAV 254

Query: 264 GRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYEDV 323
             S KA++L LGG S VIV  D D   A EG    +F +HGQ   AG+RL V E + +  
Sbjct: 255 AGSGKALTLMLGGASVVIVFEDADLDSAVEGVIDGVFTHHGQ---AGARLLVQEGLADRF 311

Query: 324 IQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPCAQ 383
             +L    E + +G  L++   +G + ++   + +   +      GA+L       P A 
Sbjct: 312 HTKLRRRIERLRIGDPLDKCTDIGALPARPELDRIAHLV--AATPGAELF--RPAPPLAD 367

Query: 384 GFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWTNDL 443
           G F  P +           +  E+ GPV VAT F   AE V  AN S +GL AS+WT + 
Sbjct: 368 GRFCAPMLITGLSPASAS-MQDEIPGPVGVATTFRTPAEAVELANNSRHGLAASVWTENG 426

Query: 444 SAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHG 485
           S AL +  +L+AG VW+N  +  D    FGG +DSG GR+ G
Sbjct: 427 SLALAVARKLKAGVVWINATHQFDAAAGFGGLRDSGFGRDGG 468



 Score = 78.6 bits (192), Expect = 8e-19
 Identities = 72/250 (28%), Positives = 111/250 (44%), Gaps = 20/250 (8%)

Query: 22  QMLIGGQWVNAQSDKTLNVYNPATGDTLTDVPDGDVEDVNAAVESAAATLQSDAWRRMPP 81
           ++ IGG+ V      +  V++ A G  L   P G+ +D+  AVE+A A   +  W     
Sbjct: 508 KLFIGGKQVRPDGGGSRAVWS-AQGRLLGHAPLGNRKDIRNAVEAARA---ATGWAATSG 563

Query: 82  SARERILLRLADLLEAHGDELA-RLETLNN--GKLLIYSKMMEVGASAQWLRYMAGWATK 138
             R ++L  +A+ L A  +E A RL  L    G+  + + +  +  +A     + G    
Sbjct: 564 YNRAQVLYYMAENLSARAEEFAARLRDLTGTPGEAEVEAAICRLFDAAASAGSVEGRVKP 623

Query: 139 LTGSTLDLSLPLPPDVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLK 198
                L ++LP              P+GVV  + P   PLL  V  +APA+A GNT VL 
Sbjct: 624 APFDGLVMALP-------------GPMGVVGILCPDAAPLLGLVSLMAPAIAMGNTCVLV 670

Query: 199 PAEETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRI 258
           P+E  PL A    ++   + LPAG +N+VTG        L  H  V  V      ++   
Sbjct: 671 PSEPFPLAATDFCQVIETSDLPAGVVNLVTGAHRDLAPTLAGHMGVDAVWCFSGADLSAA 730

Query: 259 IGSACGRSLK 268
           I +A   +LK
Sbjct: 731 IEAASAENLK 740


Lambda     K      H
   0.317    0.134    0.395 

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: 921
Number of extensions: 39
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 502
Length of database: 772
Length adjustment: 37
Effective length of query: 465
Effective length of database: 735
Effective search space:   341775
Effective search space used:   341775
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: 54 (25.4 bits)

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