Alignments for a candidate for prpE in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Shewanella sp. ANA-3

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate 7024497 Shewana3_1675 AMP-dependent synthetase and ligase (RefSeq)

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



>FitnessBrowser__ANA3:7024497
          Length = 640

 Score =  776 bits (2004), Expect = 0.0
 Identities = 371/618 (60%), Positives = 459/618 (74%), Gaps = 2/618 (0%)

Query: 12  ANPEQFWMEAAEAISWDSAPTKALTDKGDG-LYEWFADARVNTCYNAVDRHVEQGRGEQT 70
           AN + FW +AA+A+ W + P+K + D+ +   Y WF+D  +NTCYNAVDRHV  GRGEQ 
Sbjct: 19  ANKQAFWQQAAKALDWVT-PSKQILDESEAPFYHWFSDGELNTCYNAVDRHVLAGRGEQI 77

Query: 71  AIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPEALEAMLACA 130
           AI Y SP+T T+  I+Y EL+ +VA LAG L++ GV KGDRV+IYMPM+PE   AMLACA
Sbjct: 78  AIHYVSPVTETEYSITYRELQAQVARLAGYLQSVGVAKGDRVVIYMPMVPETAYAMLACA 137

Query: 131 RLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDGAIDLATHKP 190
           R+GA+HSVVFGGFAANELA RI+DA PK +++ASCG+EP   V YKPLLD A++ A HK 
Sbjct: 138 RIGAIHSVVFGGFAANELATRINDAKPKLVMSASCGIEPSGVVPYKPLLDKALNEAVHKV 197

Query: 191 DFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSGTTGQPKGVI 250
           + C+I  R Q  A++  GRD +W       + A+CV V+   P Y+LYTSGTTGQPKGV+
Sbjct: 198 EHCLILNRPQYEAQMQAGRDKDWQTALCTSDSADCVTVKATDPLYVLYTSGTTGQPKGVV 257

Query: 251 RHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTTIVFEGKPI 310
           R   G  VAL W+M NIY++  GDVFWAASDVGWVVGHSYI YGPL+ G TT+++EGKP+
Sbjct: 258 RDNGGHAVALAWSMANIYDIAQGDVFWAASDVGWVVGHSYIVYGPLLVGATTLLYEGKPV 317

Query: 311 GTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQVYLAGERADP 370
           GTPD G FWR I++++VKSFFTAPTA RA+KREDP GEF+   DLSCLK V+LAGER DP
Sbjct: 318 GTPDPGAFWRTIAKYRVKSFFTAPTAIRAIKREDPDGEFILGVDLSCLKNVFLAGERCDP 377

Query: 371 DTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPGYTVDILDEGG 430
           DT+ WA+ +L  PVIDHWWQTETGW +AAN +G+  +  K GSP  P+PGY VD++DE G
Sbjct: 378 DTLHWAEAKLHKPVIDHWWQTETGWPVAANLMGVAPIAVKAGSPGRPVPGYEVDVVDELG 437

Query: 431 HPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGMKDEDGYLYI 490
             VA    G + +KLPLPPGTL TLW    R++ SYL+ +PGYY TGDAG  DEDGYLYI
Sbjct: 438 AKVAANVSGNVVIKLPLPPGTLTTLWQNNKRYQDSYLSMYPGYYLTGDAGYMDEDGYLYI 497

Query: 491 MARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFLCLNAGCDTP 550
           M+R DD+INVAGHRLSTG  EEVL  HPDVAE AVIGV D LKGQ P+G + L  G    
Sbjct: 498 MSRIDDIINVAGHRLSTGRFEEVLCQHPDVAEAAVIGVDDKLKGQVPLGLVVLKKGVTIT 557

Query: 551 HEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGTDWKMPATID 610
            E++  Q++ LVR++IGPVA+F+L   + +LPKTRSGKILRGTM  IAD   +  PATI+
Sbjct: 558 DEELHKQLIALVRQEIGPVASFRLVSAIQKLPKTRSGKILRGTMRKIADNQQYTAPATIE 617

Query: 611 DPAILDEITTALQGLGYA 628
           DP  LD + T L  +GYA
Sbjct: 618 DPQTLDLVRTTLTRMGYA 635


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: 1315
Number of extensions: 51
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: 640
Length adjustment: 38
Effective length of query: 591
Effective length of database: 602
Effective search space:   355782
Effective search space used:   355782
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 17 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