Alignments for a candidate for pimF in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Shewanella loihica PV-4

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 5207485 Shew_0019 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= metacyc::MONOMER-20678
         (699 letters)



>FitnessBrowser__PV4:5207485
          Length = 716

 Score =  327 bits (839), Expect = 9e-94
 Identities = 227/666 (34%), Positives = 331/666 (49%), Gaps = 26/666 (3%)

Query: 23  VNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEF-GKPPQPPAL---- 77
           VN         + + ++A      V+ ++L      FI GADITEF G   Q   +    
Sbjct: 28  VNKFDRETLNSLNDALDALAQTQGVKGLMLTSGKDAFIVGADITEFLGLFAQDDNVLQGW 87

Query: 78  ----NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLPG 133
               N V   LE+ P PTI+AI G ALGGG E  L    R+A   A++GLPE KLG++PG
Sbjct: 88  LEDANKVFNKLEDLPFPTISAIKGFALGGGCETILATDLRIADTSARIGLPETKLGIIPG 147

Query: 134 AGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENLVAGAVAFAKKVLAE 191
            GGT RLPR +G + A++ I  G       ALK G ++ VV  E L   A    +  ++E
Sbjct: 148 FGGTVRLPRVIGADNALEWITTGKDQRPEAALKVGAIDAVVAPELLETAACQMLQDAISE 207

Query: 192 KRPLRRLRDDD-SKLAAAKADRSIFTNAVAAMTKKARGLE--APFACADAIGAAIDLPFE 248
           K   +  R    S L   K +  +       M  K  G    AP A  + I  A      
Sbjct: 208 KIDWQARRQRKLSPLTLPKLEAMMSFATAKGMVFKVAGKHYPAPMAVVEVIEKAALSERA 267

Query: 249 EGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGG 308
           E L+ E + F+KL  +D +KA     F   +  K        + + V+  A++GAG MGG
Sbjct: 268 EALQVEHQAFIKLAKTDVAKAL-IGIFLNDQLVKGKAKKAAKQAQAVNSAAVLGAGIMGG 326

Query: 309 GIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVG 368
           GIA   A+ G P+ + +  +  L  GL    K   A   RG   P   A  +  IT  + 
Sbjct: 327 GIAYQSASKGTPIVMKDINQAALDLGLNEAAKLLTAQINRGRSTPAKMAGVLNNITATLD 386

Query: 369 LENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDV 428
              +K AD+++EAV E   VK  V   V+      A++ SNTS +SI+ +A + ++P+  
Sbjct: 387 YNALKQADVVVEAVVEHPKVKATVLAEVEQVVGEDAIITSNTSTISINLLAKSLQKPERF 446

Query: 429 LGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAAR 488
            GMHFF+P + M L E++RG  ++ + + + V+ A K+ K P+VV  C GF  NR+L   
Sbjct: 447 CGMHFFNPVHKMPLVEVIRGEHSSEETVASVVAYAAKMGKTPIVVNDCPGFFVNRVLFPY 506

Query: 489 SKQSEKLLFEGALPQQVDAVVTK-FGMPMGPFAMGDLAGLDIGWRSR-------KDRGIK 540
                 LL +GA    +D V+ K FG PMGP  + D+ GLD G  ++        DR  K
Sbjct: 507 FAGFSGLLEDGADFAAIDKVMEKQFGWPMGPAYLLDVVGLDTGHHAQAVMAEGFPDRMAK 566

Query: 541 --SEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDE 598
              +  D + EA RFGQK GKG+Y+Y    R   P  EV+ L  + L     ++++ + +
Sbjct: 567 EGKDAIDVMFEADRFGQKNGKGFYQYSVDRRG-KPKKEVDPLSYELLGNAFGEQKEFSSD 625

Query: 599 EILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAE 658
           EI+ R + PMI E  R LEE I A P++ D+  +YG G+P +RGG   Y D++G+ +   
Sbjct: 626 EIIARTMIPMIIETVRCLEEGIIATPAEADMGLVYGLGFPPFRGGVFRYLDTLGVANFVA 685

Query: 659 RLSAYA 664
               YA
Sbjct: 686 LADQYA 691


Lambda     K      H
   0.317    0.134    0.383 

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: 1045
Number of extensions: 56
Number of successful extensions: 7
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: 699
Length of database: 716
Length adjustment: 39
Effective length of query: 660
Effective length of database: 677
Effective search space:   446820
Effective search space used:   446820
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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Protein sequences (fasta format)
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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
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