Alignments for a candidate for acs in Rhizobium etli CFN 42

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Rhizobium etli CFN 42

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011427294.1 RHE_RS21035 propionyl-CoA synthetase

Query= BRENDA::A0A0G2K047
         (683 letters)



>NCBI__GCF_000092045.1:WP_011427294.1
          Length = 636

 Score =  660 bits (1703), Expect = 0.0
 Identities = 321/630 (50%), Positives = 434/630 (68%), Gaps = 12/630 (1%)

Query: 58  YKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTS----WFVEGMLNICYNAI 113
           Y   +AA  +DPE FW +AA  I W+KP     E  Y P       WF     N C+N +
Sbjct: 5   YHQTYAAWKSDPEAFWREAAADIDWFKP----PERVYSPDEGIYGRWFSGAETNTCHNCL 60

Query: 114 DRHIENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPM 173
           DRH+  G+G + AII+DS +T  K   SY EVL +V  +A  L+  G+ +GD V++YMPM
Sbjct: 61  DRHVRAGRGGETAIIFDSAMTGEKRRFSYDEVLGEVKAIAETLLALGIARGDRVILYMPM 120

Query: 174 IPQAIYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPL 233
           +PQA+++MLACARIGA+HS++FGGFA+ EL+ RID    ++V+TAS G+EPGR V Y PL
Sbjct: 121 LPQAVFSMLACARIGAVHSVVFGGFAASELAARIDDSGARLVITASCGLEPGRVVAYKPL 180

Query: 234 LEEALRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHD--CVPVLSEHPLY 291
           +++A+ I + KP+R L+  RP + +  L+ GRD D+E  +A  +  +  CV V +  PLY
Sbjct: 181 VDQAIEIARMKPERCLVLQRPQL-RAELVGGRDEDFEAAVAPHRGAEVACVSVRATDPLY 239

Query: 292 ILYTSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGP 351
           ILYTSGTTG PKGVVR  GG+ V LNW+M +IYGLKPGEV+W ASD+GWVVGHSYI Y P
Sbjct: 240 ILYTSGTTGQPKGVVRDNGGHMVALNWSMRNIYGLKPGEVFWTASDIGWVVGHSYIVYAP 299

Query: 352 LLHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSL 411
           L+ G TT+++EGKPVGTPDAGA++R++AEH V  LFTAPTA RAIR++D    L  +Y++
Sbjct: 300 LISGVTTLIFEGKPVGTPDAGAFWRIVAEHDVRVLFTAPTAFRAIRREDGDGELIARYNM 359

Query: 412 TRFKTLFVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQA 471
              + LF+AGER D ETL+W++++  +PV+DHWWQTETG PI A+ +GLG +     G  
Sbjct: 360 PNLRALFLAGERADPETLKWAERMLAIPVIDHWWQTETGWPIAANPLGLG-ALPVKHGSP 418

Query: 472 GKCVPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYY 531
            + +PGY V +LDD    ++A +LGNIV++LPLPPG    LW   + F+  Y ++FPGYY
Sbjct: 419 AQPMPGYEVTVLDDAGHPVEAGTLGNIVIRLPLPPGCLPTLWHADDRFRSAYLDEFPGYY 478

Query: 532 DTMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKG 591
            T DAGY+DE+GYL++MSR DD+IN AGHR+S GA+EE    H  V +CAV+G  D LKG
Sbjct: 479 KTADAGYVDEDGYLFIMSRTDDIINCAGHRLSTGAMEEVCARHPDVAECAVIGVIDALKG 538

Query: 592 HVPLALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTL 651
             P    VLK+ V      +  E+V  +R  IGPVAAF+ A+ V +LPKTRSGKI R T+
Sbjct: 539 QAPCGFLVLKRHVLRESTAIEAEVVAMIRDQIGPVAAFKTAITVNRLPKTRSGKILRGTM 598

Query: 652 SALVNGKPYKVTPTIEDPSIFGHIEEVLKQ 681
             + +G P+K+  TI+DP+I   I E L++
Sbjct: 599 QKIADGIPWKMPATIDDPAILEEIAEALRK 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: 1291
Number of extensions: 64
Number of successful extensions: 4
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 Apr 09 2024. 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 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