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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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:

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:

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:

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:

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