Alignments for a candidate for pimF in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Shewanella amazonensis SB2B

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 6935814 Sama_0032 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

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



>FitnessBrowser__SB2B:6935814
          Length = 716

 Score =  340 bits (872), Expect = 1e-97
 Identities = 245/685 (35%), Positives = 341/685 (49%), Gaps = 36/685 (5%)

Query: 9   TQDQVAIVTVDSP-PVNALSAAVRRGILENVNAAV---ADPAVQAIVLVCAGRTFIAGAD 64
           T D++A +  ++P  VN       R  L ++NAA+    D   +A VL     TFI GAD
Sbjct: 13  TADKIARLCFNAPGSVNKFD----RETLASLNAALDVLKDSDAKAAVLTSGKDTFIVGAD 68

Query: 65  ITEF--------GKPPQPPA-LNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVA 115
           ITEF         K  +  A  N V   LE+ P PT++AI G ALGGG E  L   FRVA
Sbjct: 69  ITEFLALFAEEDAKLMEWIAQANVVFNKLEDLPFPTVSAIKGFALGGGCEAILATDFRVA 128

Query: 116 VKEAKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV- 174
              AK+GLPE KLGL+PG GGT RLPR +G + A++ I  G      +ALK G ++ VV 
Sbjct: 129 DTSAKIGLPETKLGLIPGFGGTVRLPRLIGADNALEWITTGKDQRPEDALKVGAIDAVVA 188

Query: 175 -ENLVAGAVAFAKKVLAEKRP--LRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLE- 230
            ENL A A+      LA K     RR R   + L   K +  +       M     G   
Sbjct: 189 PENLEAAAIQMLNDALAGKLDWQARRARKQ-APLTLPKLEAMMSFTTAKGMVYAVAGKHY 247

Query: 231 -APFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDG 289
            AP A    +  A  +   E L  E   F+KL  +D + A     F   +  K       
Sbjct: 248 PAPMAAVSVVEQAAGMSRAEALVVEHNAFIKLAKTDVATAL-IGIFLNDQLVKGKAKKAS 306

Query: 290 TKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARG 349
              + +   A++GAG MGGGIA   A+ G P+ + +  +  L  G+    K   A  ARG
Sbjct: 307 KLAKDIKHAAVLGAGIMGGGIAYQSASKGTPIVMKDINQAALDLGVNEAAKLLSAQVARG 366

Query: 350 GLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASN 409
              PD  AK +  IT  +    +KD ++++EAV E   VK  V   V+      A++ASN
Sbjct: 367 RSTPDKMAKVLNNITPALDYAPLKDVNVVVEAVVENPKVKAMVLADVENVVADDAIIASN 426

Query: 410 TSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKV 469
           TS +SID +A + K P    GMHFF+P + M L E++RG  T+ + + + V+ A K+ K 
Sbjct: 427 TSTISIDLLAKSLKNPARFCGMHFFNPVHKMPLVEVIRGKDTSEETVASVVAYASKMGKT 486

Query: 470 PVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTK-FGMPMGPFAMGDLAGLD 528
           P+VV  C GF  NR+L         LL +G     +D V+ K FG PMGP  + D+ GLD
Sbjct: 487 PIVVNDCPGFFVNRVLFPYFAGFNGLLADGGDFAAIDKVMEKQFGWPMGPAYLLDVVGLD 546

Query: 529 IGWRSR-------KDRGIKS--EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVET 579
            G  ++        DR  KS  +  D + EAGR GQK GKG+Y+Y    R   P  +V+ 
Sbjct: 547 TGHHAQAVMADGFPDRMGKSDKDAIDVMYEAGRLGQKNGKGFYQYSIDKRG-KPKKDVDP 605

Query: 580 LINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPI 639
                LA+    ++    +EI+ R + PMI E  R LEE I A P++ D+  +YG G+P 
Sbjct: 606 ASYTMLAEAFGAQKAFEADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVYGLGFPP 665

Query: 640 YRGGPMHYADSVGLKHIAERLSAYA 664
           +RGG   Y D++G+ +       YA
Sbjct: 666 FRGGVFRYLDTMGVANFVALADKYA 690


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: 1079
Number of extensions: 60
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