Alignments for a candidate for prpE in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Shewanella amazonensis SB2B

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate 6937194 Sama_1364 acyl-coenzyme A synthetase/AMP-(fatty) acid ligase (RefSeq)

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



>FitnessBrowser__SB2B:6937194
          Length = 644

 Score =  777 bits (2007), Expect = 0.0
 Identities = 367/615 (59%), Positives = 452/615 (73%)

Query: 13  NPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRHVEQGRGEQTAI 72
           NPEQ+W +AA+ + W  AP+  L      LY W+ D  +NTCYNA+DR V+ GRG QTA 
Sbjct: 25  NPEQYWRKAADMVDWHKAPSTILDSSQAPLYRWYTDGEINTCYNALDRQVDAGRGSQTAF 84

Query: 73  IYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPEALEAMLACARL 132
            Y SP+T T+  ISY E   +V  LAG L+A+GV KGDRV+IYMPM+PE   AMLACAR+
Sbjct: 85  HYVSPVTETEYSISYTECLAQVKRLAGLLKAQGVNKGDRVVIYMPMVPETAYAMLACARI 144

Query: 133 GAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDGAIDLATHKPDF 192
           GA+HSVVFGGFAANELA RI+DA P  +++ASCG+EP   V YKPLLD A+  A+HK   
Sbjct: 145 GAIHSVVFGGFAANELASRINDAKPVMVLSASCGVEPSGVVAYKPLLDAALAQASHKVSK 204

Query: 193 CVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSGTTGQPKGVIRH 252
           C+I QR Q  A +  GRD++W         A+ VPV+   P Y+LYTSGTTGQPKGV+R 
Sbjct: 205 CLILQRPQYEAAMTPGRDLDWQESVASAADADWVPVKATDPLYVLYTSGTTGQPKGVVRD 264

Query: 253 TAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTTIVFEGKPIGT 312
             G  VAL W+M+ +Y+++PGD FWAASDVGWVVGHSYI YGPLI G T++++EGKP+GT
Sbjct: 265 NGGHAVALAWSMRYLYDIEPGDTFWAASDVGWVVGHSYIVYGPLIAGATSVLYEGKPVGT 324

Query: 313 PDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQVYLAGERADPDT 372
           PDAG FWR I ++ VKSFFTAPTA RA+KREDP+G F +  +L CLKQ++LAGER DPDT
Sbjct: 325 PDAGAFWRTIKKYGVKSFFTAPTAIRAIKREDPEGFFCRNTNLDCLKQMFLAGERCDPDT 384

Query: 373 ITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPGYTVDILDEGGHP 432
           + WAQE L  PVIDHWWQTETGW +A+N +GI ++P K GSPA P+PGY VD++DE G+ 
Sbjct: 385 LLWAQEMLGKPVIDHWWQTETGWPVASNLMGIAQMPIKPGSPARPVPGYQVDVVDEAGNS 444

Query: 433 VAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGMKDEDGYLYIMA 492
           V  GE G + ++LPLPPGTLPTLW  + R+  SYL+ +P  Y TGDAG  DEDGYLYIM+
Sbjct: 445 VGAGEYGNVVIRLPLPPGTLPTLWQNDKRYIDSYLSMYPDCYLTGDAGYMDEDGYLYIMS 504

Query: 493 RTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFLCLNAGCDTPHE 552
           R DDVINVAGHRLSTG  EEVL  HP VAE AVIGV D LKGQ P+G + L  G D   E
Sbjct: 505 RIDDVINVAGHRLSTGRFEEVLCQHPAVAEAAVIGVEDKLKGQVPLGLVVLKNGVDITDE 564

Query: 553 DVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGTDWKMPATIDDP 612
            +  ++V LVR +IGPVAAFKL   + +LPKTRSGKILR TM  IAD  ++ +PATI+DP
Sbjct: 565 QLNKELVALVRSEIGPVAAFKLVSAIPKLPKTRSGKILRATMRKIADNQEYSVPATIEDP 624

Query: 613 AILDEITTALQGLGY 627
           A L+ +   L  +GY
Sbjct: 625 ATLELVRNTLTRMGY 639


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: 1344
Number of extensions: 65
Number of successful extensions: 2
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: 644
Length adjustment: 38
Effective length of query: 591
Effective length of database: 606
Effective search space:   358146
Effective search space used:   358146
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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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