Aligments for a candidate for pimF in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for pimF in Shewanella oneidensis MR-1

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 199218 SO0021 fatty oxidation complex, alpha subunit (NCBI ptt file)

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



>lcl|FitnessBrowser__MR1:199218 SO0021 fatty oxidation complex,
           alpha subunit (NCBI ptt file)
          Length = 716

 Score =  346 bits (888), Expect = 2e-99
 Identities = 239/680 (35%), Positives = 344/680 (50%), Gaps = 27/680 (3%)

Query: 10  QDQVAIVTVDSP-PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEF 68
           +D +A +  ++P  VN         +   +++      +QA+VL     TFI GADITEF
Sbjct: 14  EDNIAKLCFNAPGSVNKFDRETLASLDAALDSIKQQSNIQALVLTSGKDTFIVGADITEF 73

Query: 69  -GKPPQPPAL--------NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEA 119
            G   Q  A+        N V   LE+ P PT +AI G ALGGG E  L   FR+A   A
Sbjct: 74  LGLFAQDDAVLLSWVEQANAVFNKLEDLPFPTASAIKGFALGGGCETILATDFRIADTTA 133

Query: 120 KLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENL 177
           K+GLPE KLG++PG GGT RLPR +G + A++ I  G+   A +ALK G V+ VV  E L
Sbjct: 134 KIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGNEQRAEDALKVGAVDAVVAPEAL 193

Query: 178 VAGAVAFAKKVLAEKRPLRRLRDDD-SKLAAAKADRSIFTNAVAAMTKKARGLE--APFA 234
              A+   K  +AEK   +  R    S L   K +  +       M     G    AP A
Sbjct: 194 EVAAIQMLKDAVAEKLDWQARRQRKLSPLTLPKLEAMMSFTTAKGMVFSVAGKHYPAPMA 253

Query: 235 CADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRP 294
             + +  A      + L+ E + F+KL  +D +KA     F   +  K      G   + 
Sbjct: 254 AVNVVEQAATKGRSDALQIEHQAFIKLAKTDVAKAL-IGIFLNDQFVKGKAKKAGKLAKA 312

Query: 295 VSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPD 354
           V+  A++GAG MGGGIA   A+ G P+ + +  +  L  GL    K   A  ARG   P+
Sbjct: 313 VNSAAVLGAGIMGGGIAYQSASKGTPIVMKDIAQPALDLGLNEAAKLLSAQVARGRSTPE 372

Query: 355 APAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLS 414
             AK +  IT  +    VK AD+++EAV E   VK +V   V+ +    A++ASNTS +S
Sbjct: 373 KMAKVLNNITPALEYAPVKHADVVVEAVVEHPKVKAQVLAEVEQYVSEDAIIASNTSTIS 432

Query: 415 IDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVG 474
           I  +A + K+P+   GMHFF+P + M L E++RG  ++ + + + V+ A K+ K P+VV 
Sbjct: 433 ISLLAKSMKKPERFCGMHFFNPVHKMPLVEVIRGEHSSEETIASVVAYASKMGKTPIVVN 492

Query: 475 VCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTK-FGMPMGPFAMGDLAGLDIGWRS 533
            C GF  NR+L         LL EG     +D V+ K FG PMGP  + D+ GLD G  +
Sbjct: 493 DCPGFFVNRVLFPYFAGFNGLLAEGGDFAAIDKVMEKQFGWPMGPAYLLDVVGLDTGHHA 552

Query: 534 R-------KDRGIKS--EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDT 584
           +        DR  KS  +  D + E  R GQK GKG+Y Y   SR   P  +V+    + 
Sbjct: 553 QAVMAEGFPDRMGKSGNDAIDVMFENKRLGQKNGKGFYAYSVDSRG-KPKKDVDPTSYEL 611

Query: 585 LAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGP 644
           L     +++    +EI+ R + PMI E  R LEE I A P++ D+  +YG G+P +RGG 
Sbjct: 612 LKAAFGEQKAFDADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVYGLGFPPFRGGV 671

Query: 645 MHYADSVGLKHIAERLSAYA 664
             Y D++G+ +       YA
Sbjct: 672 FRYLDTMGVANFVALADKYA 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: 1059
Number of extensions: 57
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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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, 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

GapMind for catabolism of small carbon sources