Alignments for a candidate for acs in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Rhodobacter viridis JA737

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_110804895.1 C8J30_RS06475 propionyl-CoA synthetase

Query= BRENDA::A0A0G2K047
         (683 letters)



>NCBI__GCF_003217355.1:WP_110804895.1
          Length = 630

 Score =  662 bits (1708), Expect = 0.0
 Identities = 321/623 (51%), Positives = 430/623 (69%), Gaps = 3/623 (0%)

Query: 58  YKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHI 117
           YK  ++A  ADPE FW  AA+ I W +  +K   ++  P+  WF +GM+N C+NA+DRH+
Sbjct: 3   YKEVYSAWQADPEGFWMDAAKGIDWVQGPSKAHFDQ-GPAGEWFADGMVNTCFNAVDRHV 61

Query: 118 ENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQA 177
             G+GD+IAI+++SP+T +   I+YKE+  +VS LAG L  +GV+KGD V+IYMPMIP+A
Sbjct: 62  LAGRGDQIAIMHESPITHSTKGITYKELQARVSSLAGALRMRGVEKGDRVIIYMPMIPEA 121

Query: 178 IYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEA 237
           + AMLACARIGAIHS++FGGFA+ EL+ RID   PK ++ AS G+EPGR V Y PLL+ A
Sbjct: 122 LEAMLACARIGAIHSVVFGGFAAHELAVRIDDCTPKAIIAASCGLEPGRVVHYKPLLDAA 181

Query: 238 LRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSG 297
           + +  HKP+  +++ R   E   L+ GRD  W       +  +CVPV   HP YILYTSG
Sbjct: 182 IDLATHKPEFCVVFQR-EQEVAKLVEGRDFSWHGFQYGVKPAECVPVEGNHPAYILYTSG 240

Query: 298 TTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNT 357
           TTG PKGVVRPT G+ V LNW+M +IY ++ G+ +WAASD+GWVVGHSYICYGPLL G T
Sbjct: 241 TTGAPKGVVRPTAGHLVALNWSMKAIYNIEAGDRFWAASDVGWVVGHSYICYGPLLAGAT 300

Query: 358 TVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTL 417
           TV++EGKPVGTP AG ++R++  H + + FTAPTA+RAIR++DP     K+Y L   + L
Sbjct: 301 TVVFEGKPVGTPHAGVFWRIIQNHRIKSFFTAPTALRAIRREDPNGDYIKRYKLHEMQAL 360

Query: 418 FVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGKCVPG 477
           F+AGER D ET++W+++   VPV+DHWWQTETG  I  + +G+        G   K +PG
Sbjct: 361 FLAGERADPETVKWAQEHLGVPVIDHWWQTETGWAIAGNPLGI-ELLPVKVGSPTKPMPG 419

Query: 478 YNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAG 537
           Y+V +LD+    +   +LG I +KLPLPPG    LW   + FK  Y   FPGYY+T DAG
Sbjct: 420 YDVQVLDEGGHPVAPGTLGAIAIKLPLPPGTLPTLWNADDRFKKSYLSHFPGYYETGDAG 479

Query: 538 YMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLAL 597
           Y+DE+GY+Y+M+R DDVINVAGHR+S GA+EE + SH  V +CAV+G  D LKG +P+  
Sbjct: 480 YIDEDGYVYIMARTDDVINVAGHRLSTGAMEEVLASHKDVAECAVIGVADELKGQLPMGF 539

Query: 598 CVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNG 657
             L K        V++E V+ VR  IGPVAAF+ AV V +LPKTRSGKI R T++ + +G
Sbjct: 540 LCLTKGCTRPAADVIKECVRLVRDQIGPVAAFKLAVVVDRLPKTRSGKILRGTMAKIADG 599

Query: 658 KPYKVTPTIEDPSIFGHIEEVLK 680
             YK+  TI+DP+I   I   LK
Sbjct: 600 VEYKMPATIDDPAILDEITAALK 622


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: 1396
Number of extensions: 66
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: 630
Length adjustment: 38
Effective length of query: 645
Effective length of database: 592
Effective search space:   381840
Effective search space used:   381840
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 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