Alignments for a candidate for paaH in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Shewanella oneidensis MR-1

Align Enoyl-CoA hydratase (EC 4.2.1.17); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate 199218 SO0021 fatty oxidation complex, alpha subunit (NCBI ptt file)

Query= reanno::ANA3:7022769
         (716 letters)



>FitnessBrowser__MR1:199218
          Length = 716

 Score = 1376 bits (3561), Expect = 0.0
 Identities = 702/716 (98%), Positives = 709/716 (99%)

Query: 1   MIYQSPTIQVELLEDNIAKLCFNAPGSVNKFDRETLASLDAALDSIKQQSNIQALVLTSG 60
           MIYQSPTIQVELLEDNIAKLCFNAPGSVNKFDRETLASLDAALDSIKQQSNIQALVLTSG
Sbjct: 1   MIYQSPTIQVELLEDNIAKLCFNAPGSVNKFDRETLASLDAALDSIKQQSNIQALVLTSG 60

Query: 61  KDTFIVGADITEFLGLFAQDDAVLLSWIEQANAVFNKLEDLPFPTASAIKGFALGGGCET 120
           KDTFIVGADITEFLGLFAQDDAVLLSW+EQANAVFNKLEDLPFPTASAIKGFALGGGCET
Sbjct: 61  KDTFIVGADITEFLGLFAQDDAVLLSWVEQANAVFNKLEDLPFPTASAIKGFALGGGCET 120

Query: 121 ILATDFRIADTTAKIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGKDQRPEDALK 180
           ILATDFRIADTTAKIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTG +QR EDALK
Sbjct: 121 ILATDFRIADTTAKIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGNEQRAEDALK 180

Query: 181 VGAVDAVVAPEALEAAAIQMLKDAVAEKLDWQARRQRKMSPLTLPKLEAMMSFTTAKGMV 240
           VGAVDAVVAPEALE AAIQMLKDAVAEKLDWQARRQRK+SPLTLPKLEAMMSFTTAKGMV
Sbjct: 181 VGAVDAVVAPEALEVAAIQMLKDAVAEKLDWQARRQRKLSPLTLPKLEAMMSFTTAKGMV 240

Query: 241 FAVAGKHYPAPMAAVSVVEQAATKGRSDALQIEHQAFIKLAKTDVAKALIGIFLNDQLVK 300
           F+VAGKHYPAPMAAV+VVEQAATKGRSDALQIEHQAFIKLAKTDVAKALIGIFLNDQ VK
Sbjct: 241 FSVAGKHYPAPMAAVNVVEQAATKGRSDALQIEHQAFIKLAKTDVAKALIGIFLNDQFVK 300

Query: 301 GKAKKAGKLAKDVKSAAVLGAGIMGGGIAYQSASKGTPIVMKDIAQPALDLGLGEAAKLL 360
           GKAKKAGKLAK V SAAVLGAGIMGGGIAYQSASKGTPIVMKDIAQPALDLGL EAAKLL
Sbjct: 301 GKAKKAGKLAKAVNSAAVLGAGIMGGGIAYQSASKGTPIVMKDIAQPALDLGLNEAAKLL 360

Query: 361 SAQVARGRSTPEKMAKVLNNITPALDYAPVKHADVVVEAVVEHPKVKAQVLAEVEQYVSE 420
           SAQVARGRSTPEKMAKVLNNITPAL+YAPVKHADVVVEAVVEHPKVKAQVLAEVEQYVSE
Sbjct: 361 SAQVARGRSTPEKMAKVLNNITPALEYAPVKHADVVVEAVVEHPKVKAQVLAEVEQYVSE 420

Query: 421 DAIIASNTSTISINLLAKSMKKPERFCGMHFFNPVHKMPLVEVIRGEHSSEETIASVVAY 480
           DAIIASNTSTISI+LLAKSMKKPERFCGMHFFNPVHKMPLVEVIRGEHSSEETIASVVAY
Sbjct: 421 DAIIASNTSTISISLLAKSMKKPERFCGMHFFNPVHKMPLVEVIRGEHSSEETIASVVAY 480

Query: 481 ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFNGLLAEGGDFAAIDKVMEKQFGWPMGPAYL 540
           ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFNGLLAEGGDFAAIDKVMEKQFGWPMGPAYL
Sbjct: 481 ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFNGLLAEGGDFAAIDKVMEKQFGWPMGPAYL 540

Query: 541 LDVVGLDTGHHAQAVMAEGFPDRMGKSGNDAIDVMFENKRLGQKNGKGFYAYSVDSRGKP 600
           LDVVGLDTGHHAQAVMAEGFPDRMGKSGNDAIDVMFENKRLGQKNGKGFYAYSVDSRGKP
Sbjct: 541 LDVVGLDTGHHAQAVMAEGFPDRMGKSGNDAIDVMFENKRLGQKNGKGFYAYSVDSRGKP 600

Query: 601 KKDVDPTSYELLKAAFGEQKAFDADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVY 660
           KKDVDPTSYELLKAAFGEQKAFDADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVY
Sbjct: 601 KKDVDPTSYELLKAAFGEQKAFDADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVY 660

Query: 661 GLGFPPFRGGVFRYLDTMGVANFVALADKYAHLGGLYQVTDAMRALAANNGSYYQA 716
           GLGFPPFRGGVFRYLDTMGVANFVALADKYAHLGGLYQVTDAMRALAANNGSYYQA
Sbjct: 661 GLGFPPFRGGVFRYLDTMGVANFVALADKYAHLGGLYQVTDAMRALAANNGSYYQA 716


Lambda     K      H
   0.318    0.135    0.384 

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: 1636
Number of extensions: 56
Number of successful extensions: 1
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: 716
Length of database: 716
Length adjustment: 40
Effective length of query: 676
Effective length of database: 676
Effective search space:   456976
Effective search space used:   456976
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: 55 (25.8 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, or view the source code.

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