Alignments for a candidate for prpE in Rhodobacter ovatus JA234

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Rhodobacter ovatus JA234

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_097030583.1 CRO07_RS09625 propionyl-CoA synthetase

Query= reanno::Phaeo:GFF1175
         (629 letters)



>NCBI__GCF_900207575.1:WP_097030583.1
          Length = 630

 Score = 1009 bits (2609), Expect = 0.0
 Identities = 480/629 (76%), Positives = 545/629 (86%)

Query: 1   MSYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDR 60
           M+Y+ +Y+    +P  FWM+AAE I W S P+KAL +     YEWFAD  VNTC+NAVDR
Sbjct: 1   MAYASLYKWSLEDPNGFWMKAAEEIDWVSPPSKALFEDKAPFYEWFADGMVNTCWNAVDR 60

Query: 61  HVEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIP 120
           HVE GRG+Q AI+++SPITH+ + I+Y EL+ RVA+LAGALRAKG+EKGDRVIIYMPMIP
Sbjct: 61  HVEAGRGKQIAIVHESPITHSSKGITYAELQARVASLAGALRAKGIEKGDRVIIYMPMIP 120

Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLD 180
           EALEAMLACARLGA+HSVVFGGFAA+ELAVRIDD  PKAIIAASCGLEP R VHYKPLLD
Sbjct: 121 EALEAMLACARLGAIHSVVFGGFAAHELAVRIDDCKPKAIIAASCGLEPSRVVHYKPLLD 180

Query: 181 GAIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTS 240
            AI+ ATHKPDFCVIFQREQEVA+L+EGRDV WH FQYGVEPAECVPVEGNHPAYILYTS
Sbjct: 181 QAIEEATHKPDFCVIFQREQEVAKLVEGRDVAWHTFQYGVEPAECVPVEGNHPAYILYTS 240

Query: 241 GTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGN 300
           GTTGQPKGV+R T G LVAL WTMK IY+++ GDVFWAASDVGWVVGHSYICYGPLI G 
Sbjct: 241 GTTGQPKGVVRATGGHLVALKWTMKAIYDINAGDVFWAASDVGWVVGHSYICYGPLIAGA 300

Query: 301 TTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQ 360
           TTIV+EGKP+GTPDAG FWRV+  +KVK+FFTAPTA RA+KREDP+G+ ++ Y+L  LK 
Sbjct: 301 TTIVYEGKPVGTPDAGAFWRVMQNNKVKTFFTAPTALRAIKREDPQGKLIEDYNLRSLKA 360

Query: 361 VYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPG 420
           ++LAGERADPDT+ WAQ  L VPV+D+WWQTETGW+IAANP+GI++LP K+GSP VPMPG
Sbjct: 361 LFLAGERADPDTVVWAQRNLNVPVVDNWWQTETGWAIAANPIGIQQLPVKIGSPTVPMPG 420

Query: 421 YTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAG 480
           Y V +LDEGGH +  GELGAIA+KLPLPPGTLPTLWNAE+RFKKSYL+ FPGYYETGDAG
Sbjct: 421 YDVRVLDEGGHQLGAGELGAIAIKLPLPPGTLPTLWNAEERFKKSYLSHFPGYYETGDAG 480

Query: 481 MKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGF 540
             DEDGY+YIMARTDDVINVAGHRLSTGAMEE+LA H DVAECAVIGVSD+LKGQ+P+GF
Sbjct: 481 YIDEDGYVYIMARTDDVINVAGHRLSTGAMEEILASHTDVAECAVIGVSDALKGQSPLGF 540

Query: 541 LCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600
           LCLN G      DVV + V+LVR+KIGPVA FK ACVVDRLPKTRSGKILRGTMV IADG
Sbjct: 541 LCLNKGSGREPADVVKECVQLVRDKIGPVADFKRACVVDRLPKTRSGKILRGTMVKIADG 600

Query: 601 TDWKMPATIDDPAILDEITTALQGLGYAK 629
            D+KMPATIDDPAILDEI  +L  +GY K
Sbjct: 601 QDFKMPATIDDPAILDEIRESLLEMGYPK 629


Lambda     K      H
   0.318    0.137    0.428 

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: 1526
Number of extensions: 60
Number of successful extensions: 1
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: 629
Length of database: 630
Length adjustment: 38
Effective length of query: 591
Effective length of database: 592
Effective search space:   349872
Effective search space used:   349872
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