Alignments for a candidate for acs in Brucella inopinata BO1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Brucella inopinata BO1

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_008507389.1 BIBO1_RS12015 propionyl-CoA synthetase

Query= BRENDA::A0A0G2K047
         (683 letters)



>NCBI__GCF_000182725.1:WP_008507389.1
          Length = 636

 Score =  682 bits (1759), Expect = 0.0
 Identities = 317/625 (50%), Positives = 441/625 (70%), Gaps = 4/625 (0%)

Query: 57  EYKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRH 116
           +Y   +AA   DPE FW  AA  I W+KPW +           W+     N CYNA+DRH
Sbjct: 4   KYAETYAAWQNDPEGFWADAAAAIDWFKPWEQVFAGGEGTYGRWYTGAECNTCYNALDRH 63

Query: 117 IENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQ 176
           + NG+GD++A+IY+SP+T     I+Y+E+LE+V  LA V++  GV+K D V+IYMP +P+
Sbjct: 64  VANGRGDQLALIYESPITGKTRKITYRELLEEVEALAAVMLDNGVQKSDRVLIYMPTVPE 123

Query: 177 AIYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEE 236
           A+ AMLA ARIGAIHS++FGGFA+ EL+TRID  KP +++ AS GIEP R V Y  +L++
Sbjct: 124 AVVAMLASARIGAIHSVVFGGFAANELATRIDDAKPVMIIAASCGIEPSRVVPYQAMLDK 183

Query: 237 ALRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEE--EMAKAQSHDCVPVLSEHPLYILY 294
           A+ +  HK D  +I+ R     +P+  GRD+D+ E  + A+ +   CVPV +  PLY+LY
Sbjct: 184 AISLAHHKVDHCIIFQREQHRHLPV-EGRDIDYREAVDAARGRHVPCVPVAATDPLYVLY 242

Query: 295 TSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLH 354
           TSGTTG PKGVVR  GG+ V L W+M  ++ +KPG+VWWAASD+GWVVGHSYI Y PLL 
Sbjct: 243 TSGTTGEPKGVVRDNGGHMVALVWSMKHVFDVKPGQVWWAASDVGWVVGHSYIVYAPLLI 302

Query: 355 GNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRF 414
           G T++L+EGKPVGTPDAG Y+R++ EHGV  +FTAPTA+RAI+++D      +++ L+ F
Sbjct: 303 GATSILFEGKPVGTPDAGEYWRIIEEHGVEVMFTAPTALRAIKKEDADGHFVRRHDLSGF 362

Query: 415 KTLFVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGKC 474
           + L++AGER D +T+ W++ +   PV+DHWWQTE+G P+ A+ +GLG  +T   G    C
Sbjct: 363 RALYLAGERADPDTIHWAENLLGCPVIDHWWQTESGWPMVANPLGLGLLET-KYGSPAVC 421

Query: 475 VPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTM 534
           +PGY++ +LDD   +++  +LGNI++KLPLPPG    LW   E F+  Y  +FPGYY T 
Sbjct: 422 LPGYDIRVLDDEGHEVEPGTLGNILIKLPLPPGCLPTLWNADERFRKAYLNEFPGYYKTA 481

Query: 535 DAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVP 594
           DAGYMDE+GYLY+MSR DD+INVAGHR+S GA+EE + SH  V +CAV+G  DPLKG VP
Sbjct: 482 DAGYMDEDGYLYIMSRTDDIINVAGHRLSTGAMEEVLSSHPDVAECAVLGISDPLKGQVP 541

Query: 595 LALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSAL 654
               VLK +++   ++V +E +  +R +IGPVAAFR A+ +K+LPKTRSGKI RST+  +
Sbjct: 542 CGFLVLKSNIDRDPQEVEKECISMIRDAIGPVAAFRLALAIKRLPKTRSGKILRSTIQKM 601

Query: 655 VNGKPYKVTPTIEDPSIFGHIEEVL 679
            +G+ +K+  TI+DP+I   I  +L
Sbjct: 602 ADGQEWKMPATIDDPAILDEIGTIL 626


Lambda     K      H
   0.318    0.136    0.421 

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: 1324
Number of extensions: 67
Number of successful extensions: 3
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: 683
Length of database: 636
Length adjustment: 38
Effective length of query: 645
Effective length of database: 598
Effective search space:   385710
Effective search space used:   385710
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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