Alignments for a candidate for pimF in Xenophilus azovorans DSM 13620

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Xenophilus azovorans DSM 13620

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_038200266.1 Q392_RS00345 fatty acid oxidation complex subunit alpha FadB

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



>NCBI__GCF_000745855.1:WP_038200266.1
          Length = 715

 Score =  353 bits (906), Expect = e-101
 Identities = 245/697 (35%), Positives = 351/697 (50%), Gaps = 35/697 (5%)

Query: 14  AIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFGKP-- 71
           AI  +D   V     AVR         A A   V+ +++  A   FI GADITEFG+   
Sbjct: 27  AINKLDDKAVAEFDQAVRA-------IAAAGGGVRGVLVTSAKDVFIVGADITEFGRKFR 79

Query: 72  -------PQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLP 124
                   +    N V    E+   P + AI+G ALGGGLE+AL    RV  + A++G+P
Sbjct: 80  RGGEQVAREVLEANQVFVRFEDLDVPAVVAINGFALGGGLELALCASHRVMSEHARIGVP 139

Query: 125 EVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENLVAGAV 182
           EVKLGL PG GGT RL R  GP+ AV  +  G  I A EAL+ G+V+ V   E L   A+
Sbjct: 140 EVKLGLFPGFGGTVRLARVGGPQAAVDWVASGRSIKADEALRAGVVDAVAAPERLRDEAL 199

Query: 183 AFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKA-RGLEAPFACADAIGA 241
           A   + + E R   R      + A   ADR +F +A+A + + A R   A       + A
Sbjct: 200 AVLWQCV-EGRLDWRAAQQKKRAAVPAADRRVFDDALAQLARHASRHQPAAEMAVHMMRA 258

Query: 242 AIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAII 301
           A        L  E E F  +  +  +++   AF  E +A K          R V + A+I
Sbjct: 259 AAGEDRARALAMEAEAFGAVTQTQAARSMVQAFLNE-QAVKKRARSQAEGGRTVRQAAVI 317

Query: 302 GAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMA 361
           GAG MGGGIA + A  G  V L +     L+ G+   ++       +G L  +   +   
Sbjct: 318 GAGIMGGGIAYTTALRGTAVRLKDIAPAALELGVNEARRQLAKQVQQGRLTQEKADRIAG 377

Query: 362 LITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAAT 421
            IT  +    +   D+++EAV E++ VK  V TA++ H +PG VLASNTS L ID+IAA 
Sbjct: 378 AITPQLDDAGLDAVDIVVEAVVESLPVKHRVLTALEEHVRPGTVLASNTSSLRIDDIAAP 437

Query: 422 TKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVG 481
             RP+DV+G+HFF+P  VM L E+VRG +++  A+ TA +    + K P+VV  C GF+ 
Sbjct: 438 LARPEDVVGLHFFNPVPVMPLVEVVRGTRSSDAAVATATAHVIGLGKTPIVVKDCPGFLV 497

Query: 482 NRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLD----------IGW 531
           NR+L         L+ +GA  +++D  +  FG PMGP  + D+ GLD           G+
Sbjct: 498 NRILTPYVLSFCDLVAQGADHERIDRALEAFGWPMGPAYLEDVVGLDTGSHVIDVISAGY 557

Query: 532 RSRKDRGIKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLK 591
             R   G ++ I  A  EAGR GQK+G G+Y Y+     P      E        + G  
Sbjct: 558 PQRMHPGERNVIR-AFAEAGRLGQKSGAGFYDYDAAGGRPKRSSSAEARALVRQMQRGAV 616

Query: 592 RRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSV 651
              + D +I+ERM+ PM+ E  R LEE +    +++D   L G G+P Y GGP+ YAD +
Sbjct: 617 -CGLDDAQIVERMMLPMLLEAIRCLEEGVVRTAAELDQAMLLGVGFPAYLGGPLQYADWL 675

Query: 652 GLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688
           GL  +A R ++ A     P  E   LL+ +AA+G +F
Sbjct: 676 GLPRLAARCASLAAC--GPMFEAPALLSEMAAQGGSF 710


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: 1047
Number of extensions: 44
Number of successful extensions: 6
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: 715
Length adjustment: 39
Effective length of query: 660
Effective length of database: 676
Effective search space:   446160
Effective search space used:   446160
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 Apr 09 2024. 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 2024 update 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