Alignments for a candidate for pimF in Azospirillum sp. B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Azospirillum sp. B510

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_148219526.1 AZL_RS21225 fatty acid oxidation complex subunit alpha FadB

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



>NCBI__GCF_000010725.1:WP_148219526.1
          Length = 721

 Score =  355 bits (911), Expect = e-102
 Identities = 243/688 (35%), Positives = 363/688 (52%), Gaps = 36/688 (5%)

Query: 35  LENVNAAVA----DPAVQAIVLVCAGRTFIAGADITEF----GKPPQPPALND-----VI 81
           L+ +N A+     D  V  +++     +FI GADI EF    G      A+++     VI
Sbjct: 36  LDELNRALCLVREDRTVTGLLITSGKDSFIVGADIFEFTDLFGMAEDEIAIHNAGQSAVI 95

Query: 82  AALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLPGAGGTQRLP 141
            AL + P PT+ A++G ALGGGLE+AL    R+    A++GLPEV LG+ PG GGT RLP
Sbjct: 96  TALADLPVPTVVAVNGLALGGGLELALAADVRMLSDSARIGLPEVGLGIFPGFGGTVRLP 155

Query: 142 RAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE--NLVAGAVAFAKKVLAEKRPLRRLR 199
           R +G E A+Q I+ G+P  A +AL+ G V+ VV    L   A+     ++A      R +
Sbjct: 156 RLIGVEAALQWIMSGTPRKADDALRAGAVDAVVPPPELREAALERLHGLVASPDWSERRK 215

Query: 200 DDDSKLAAAKADRS-IFTNAVAAMTKKARGLEAPFACADAIGAAIDLPFEEGLKKEREGF 258
           +  S +  A  D + IF  A A   K    L A  A  + I +A  +  +  L  E   F
Sbjct: 216 EALSPVVRAGEDLAPIFAAAKAKARKTGPHLPASLAVVELIESAAGVDRDAALALEARAF 275

Query: 259 MKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAG 318
             +  +  ++A   A F   +A K          RPVSR A++GAG MGGGIA   A  G
Sbjct: 276 AHIARTPAARAL-VAVFINDQAVKKTTKQQTRAARPVSRAAVLGAGIMGGGIAYQSAVCG 334

Query: 319 IPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLI 378
           IPV + +  +  L  G+             G L        +A I   +  + + +AD+I
Sbjct: 335 IPVIMKDIAQSALDLGMTQAGALLAKRVETGALSSAKADGILASIRPGLTYDGIAEADVI 394

Query: 379 IEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPAN 438
           +EAV E +A+K+ V   ++ H +P AV+A+NTS L + ++A   + P++ +GMHFF+P +
Sbjct: 395 VEAVVENIAIKRAVLAELEEHIRPDAVVATNTSSLLVADLARDLEWPENFVGMHFFNPVH 454

Query: 439 VMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFE 498
            M L E+++G  T+P+A+ T V  A  + K PVVV  C GF+ NR+LAA      +L+ +
Sbjct: 455 RMPLVEVIQGPHTSPEAVATIVGYASAMGKTPVVVRDCPGFLVNRILAANVLGFLRLIHD 514

Query: 499 GALPQQVDAVVTKFGMPMGPFAMGDLAGLD----------IGWRSRKDRGIKSEIADALC 548
           GA   ++DA +  FG PMGP  + D+ G+D           G+  R  R   +   D + 
Sbjct: 515 GADFLRIDAAMEGFGWPMGPAWLQDVIGMDTSRHVIEVIAAGYPERM-RVEFATALDVMV 573

Query: 549 EAGRFGQKTGKGYYKYE---QGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERMV 605
           E+ RFGQK+G G+Y+YE    G +  + DP+V  L+  T+   G   R I+DEEI++R +
Sbjct: 574 ESKRFGQKSGAGFYRYEADAAGHQRKVVDPDVGALL-ATVQPGG--SRIISDEEIVQRTM 630

Query: 606 YPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAK 665
            PMI E AR LE+ +    ++ D+  + G G+P + GG +HYAD +G K I E    YA 
Sbjct: 631 LPMILETARCLEDGVVGSAAEADMALILGIGFPRHLGGALHYADELGAKTIMEWCDRYAN 690

Query: 666 ATNDPSLEPAPLLARLAAEGKTFASLTQ 693
               P   P P + RLA +G  +A+L Q
Sbjct: 691 L--GPLYHPTPRMRRLAVDGAGWANLVQ 716


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: 1095
Number of extensions: 61
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: 721
Length adjustment: 39
Effective length of query: 660
Effective length of database: 682
Effective search space:   450120
Effective search space used:   450120
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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