GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Shewanella loihica PV-4

Align Enoyl-CoA hydratase (EC 4.2.1.17); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate 5207485 Shew_0019 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

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



>lcl|FitnessBrowser__PV4:5207485 Shew_0019 multifunctional fatty
           acid oxidation complex subunit alpha (RefSeq)
          Length = 716

 Score = 1216 bits (3145), Expect = 0.0
 Identities = 614/716 (85%), Positives = 651/716 (90%)

Query: 1   MIYQSPTIQVELLEDNIAKLCFNAPGSVNKFDRETLASLDAALDSIKQQSNIQALVLTSG 60
           MIYQSPTIQVELLEDNIA+LCFNA GSVNKFDRETL SL+ ALD++ Q   ++ L+LTSG
Sbjct: 1   MIYQSPTIQVELLEDNIARLCFNAEGSVNKFDRETLNSLNDALDALAQTQGVKGLMLTSG 60

Query: 61  KDTFIVGADITEFLGLFAQDDAVLLSWIEQANAVFNKLEDLPFPTASAIKGFALGGGCET 120
           KD FIVGADITEFLGLFAQDD VL  W+E AN VFNKLEDLPFPT SAIKGFALGGGCET
Sbjct: 61  KDAFIVGADITEFLGLFAQDDNVLQGWLEDANKVFNKLEDLPFPTISAIKGFALGGGCET 120

Query: 121 ILATDFRIADTTAKIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGKDQRPEDALK 180
           ILATD RIADT+A+IGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGKDQRPE ALK
Sbjct: 121 ILATDLRIADTSARIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGKDQRPEAALK 180

Query: 181 VGAVDAVVAPEALEAAAIQMLKDAVAEKLDWQARRQRKMSPLTLPKLEAMMSFTTAKGMV 240
           VGA+DAVVAPE LE AA QML+DA++EK+DWQARRQRK+SPLTLPKLEAMMSF TAKGMV
Sbjct: 181 VGAIDAVVAPELLETAACQMLQDAISEKIDWQARRQRKLSPLTLPKLEAMMSFATAKGMV 240

Query: 241 FAVAGKHYPAPMAAVSVVEQAATKGRSDALQIEHQAFIKLAKTDVAKALIGIFLNDQLVK 300
           F VAGKHYPAPMA V V+E+AA   R++ALQ+EHQAFIKLAKTDVAKALIGIFLNDQLVK
Sbjct: 241 FKVAGKHYPAPMAVVEVIEKAALSERAEALQVEHQAFIKLAKTDVAKALIGIFLNDQLVK 300

Query: 301 GKAKKAGKLAKDVKSAAVLGAGIMGGGIAYQSASKGTPIVMKDIAQPALDLGLGEAAKLL 360
           GKAKKA K A+ V SAAVLGAGIMGGGIAYQSASKGTPIVMKDI Q ALDLGL EAAKLL
Sbjct: 301 GKAKKAAKQAQAVNSAAVLGAGIMGGGIAYQSASKGTPIVMKDINQAALDLGLNEAAKLL 360

Query: 361 SAQVARGRSTPEKMAKVLNNITPALDYAPVKHADVVVEAVVEHPKVKAQVLAEVEQYVSE 420
           +AQ+ RGRSTP KMA VLNNIT  LDY  +K ADVVVEAVVEHPKVKA VLAEVEQ V E
Sbjct: 361 TAQINRGRSTPAKMAGVLNNITATLDYNALKQADVVVEAVVEHPKVKATVLAEVEQVVGE 420

Query: 421 DAIIASNTSTISINLLAKSMKKPERFCGMHFFNPVHKMPLVEVIRGEHSSEETIASVVAY 480
           DAII SNTSTISINLLAKS++KPERFCGMHFFNPVHKMPLVEVIRGEHSSEET+ASVVAY
Sbjct: 421 DAIITSNTSTISINLLAKSLQKPERFCGMHFFNPVHKMPLVEVIRGEHSSEETVASVVAY 480

Query: 481 ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFNGLLAEGGDFAAIDKVMEKQFGWPMGPAYL 540
           A+KMGKTPIVVNDCPGFFVNRVLFPYFAGF+GLL +G DFAAIDKVMEKQFGWPMGPAYL
Sbjct: 481 AAKMGKTPIVVNDCPGFFVNRVLFPYFAGFSGLLEDGADFAAIDKVMEKQFGWPMGPAYL 540

Query: 541 LDVVGLDTGHHAQAVMAEGFPDRMGKSGNDAIDVMFENKRLGQKNGKGFYAYSVDSRGKP 600
           LDVVGLDTGHHAQAVMAEGFPDRM K G DAIDVMFE  R GQKNGKGFY YSVD RGKP
Sbjct: 541 LDVVGLDTGHHAQAVMAEGFPDRMAKEGKDAIDVMFEADRFGQKNGKGFYQYSVDRRGKP 600

Query: 601 KKDVDPTSYELLKAAFGEQKAFDADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVY 660
           KK+VDP SYELL  AFGEQK F +DEIIARTMIPMIIETVRCLEEGI+A+PAEADMGLVY
Sbjct: 601 KKEVDPLSYELLGNAFGEQKEFSSDEIIARTMIPMIIETVRCLEEGIIATPAEADMGLVY 660

Query: 661 GLGFPPFRGGVFRYLDTMGVANFVALADKYAHLGGLYQVTDAMRALAANNGSYYQA 716
           GLGFPPFRGGVFRYLDT+GVANFVALAD+YAHLGGLYQVTD MR LAA NGSYY A
Sbjct: 661 GLGFPPFRGGVFRYLDTLGVANFVALADQYAHLGGLYQVTDKMRELAATNGSYYPA 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: 1508
Number of extensions: 50
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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