GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PV4:5207485
          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:

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