Alignments for a candidate for acs in Rhizobium grahamii CCGE 502

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Rhizobium grahamii CCGE 502

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_016556838.1 RGCCGE502_RS24215 propionyl-CoA synthetase

Query= BRENDA::A0A0G2K047
         (683 letters)



>NCBI__GCF_000298315.2:WP_016556838.1
          Length = 636

 Score =  655 bits (1689), Expect = 0.0
 Identities = 319/628 (50%), Positives = 429/628 (68%), Gaps = 4/628 (0%)

Query: 56  GEYKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDR 115
           G Y+  +A    DPE FW +AA +I W+K    T      P   WF  G  N CYN +DR
Sbjct: 3   GGYQRTYARWKDDPEAFWQEAAAEIDWFKEPELTFSREGGPYGRWFPGGETNTCYNCLDR 62

Query: 116 HIENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIP 175
           H+  G+G   A IYDSP+   K   SY EVL +VS +A  L ++G+ KGD V+IYMPM+P
Sbjct: 63  HVRAGRGGDTAFIYDSPIGGAKTIFSYGEVLAEVSAIAATLRERGIGKGDRVIIYMPMVP 122

Query: 176 QAIYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLE 235
           QA+++MLACARIGA+HS++FGGFA+ EL+ RID    K++VTAS G+EPGR V Y PL++
Sbjct: 123 QAVFSMLACARIGAVHSVVFGGFAANELAARIDDSGAKLIVTASCGLEPGRVVPYKPLVD 182

Query: 236 EALRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSH--DCVPVLSEHPLYIL 293
           +A+ I + KP   L+  RP +    L+ GRD D+E  +A+ +    +CV + +   LYIL
Sbjct: 183 QAIAIAKSKPAHCLVLQRPQLA-ADLVDGRDEDFEAAVARNRGVKVECVSLGATDELYIL 241

Query: 294 YTSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLL 353
           YTSGTTG PKGVVR  GG+ V LNW+M++I+G++ GEV+WAASD+GWVVGHSYI Y PLL
Sbjct: 242 YTSGTTGQPKGVVRDNGGHMVALNWSMANIFGIRQGEVFWAASDIGWVVGHSYIVYAPLL 301

Query: 354 HGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTR 413
            G T+V++EGKPVGTPDAG ++R+ +EH V  LFTAPTA RAIR++D      K YS+  
Sbjct: 302 AGATSVIFEGKPVGTPDAGVFWRIASEHDVRVLFTAPTAFRAIRREDSEGVHLKTYSMPN 361

Query: 414 FKTLFVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGK 473
           F+ LF+AGER D ETL+W++++  VPV+DHWWQTETG P+ A+ +GL        G    
Sbjct: 362 FRALFLAGERADPETLKWAERMLDVPVIDHWWQTETGWPMVANPLGL-EVLPVKHGSPSV 420

Query: 474 CVPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDT 533
            +PGY++ +LDD    +   +LGN+VV+LPLPPG    LW     F   Y  +FPGYY T
Sbjct: 421 PMPGYSIHVLDDAGHAVAPGTLGNVVVQLPLPPGCLPTLWNADARFHSAYLAEFPGYYKT 480

Query: 534 MDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHV 593
            DAGY+DE+GYL++MSR DD+IN AGHR+S GA+EE   +H  V +CAVVG  D LKG V
Sbjct: 481 ADAGYIDEDGYLFIMSRTDDIINCAGHRLSTGAMEEVCATHPDVAECAVVGIADQLKGQV 540

Query: 594 PLALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSA 653
           P    +LKK+V+     +  E+V+ +R++IGPVAAF+ A+ V +LPKTRSGKI R T+  
Sbjct: 541 PCGFLILKKNVSRETSAIESEVVQLIREAIGPVAAFKTAITVDRLPKTRSGKILRGTIQK 600

Query: 654 LVNGKPYKVTPTIEDPSIFGHIEEVLKQ 681
           + +G P+K+  TI+DP I   I E L++
Sbjct: 601 IADGVPWKMPATIDDPVILEEIAEALRK 628


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: 1278
Number of extensions: 59
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)
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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