Alignments for a candidate for prpE in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Shewanella loihica PV-4

Align propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate 5210124 Shew_2568 AMP-dependent synthetase and ligase (RefSeq)

Query= metacyc::MONOMER-21334
         (629 letters)



>FitnessBrowser__PV4:5210124
          Length = 662

 Score =  815 bits (2104), Expect = 0.0
 Identities = 394/626 (62%), Positives = 475/626 (75%)

Query: 3   YQDVYESWKSDPEAFWMEAAKSIDWVEAPSRALDDSNAPLYEWFTDAKVNTCWNAVDRHV 62
           +  +++    +P AFW EAA ++ W +   R LDDS AP+Y WF+  ++NTC+NAVDRHV
Sbjct: 33  HNQLHQESIDNPNAFWGEAAGALAWDKTFERVLDDSQAPMYRWFSGGQLNTCYNAVDRHV 92

Query: 63  EAGRGEQTAIIYDSPITHTKRQISYVELRNRVAMLAGALRAKGVEKGDRVIIYMPMIPEA 122
           EAGRGEQ AI Y SPIT T+  I+Y EL+ +V+ LAG + ++GV KGDRVIIYMPM+PE 
Sbjct: 93  EAGRGEQVAIQYVSPITGTEYGITYNELQAQVSRLAGYMASQGVVKGDRVIIYMPMVPET 152

Query: 123 LEAMLACARLGAVHSVVFGGFAANELAVRIDDAQPKAIIAASCGLEPGRVVHYKPLLDGA 182
             AMLACARLGA+HSVVFGGFAANELA RIDDA PK I++ASCG+EP  VV YKPLLD A
Sbjct: 153 AYAMLACARLGAIHSVVFGGFAANELATRIDDATPKMILSASCGVEPSGVVAYKPLLDDA 212

Query: 183 IDMAKHKPEFCVIFQREQEVAHLEEGRDYNWHGFQYGVEPAECVPVEGNHPAYILYTSGT 242
           ++ A HK E CVI  R Q  A L +GRD +W G        EC  VE   P YILYTSGT
Sbjct: 213 LEQASHKVEQCVILNRPQLQADLVDGRDVDWQGAMADAPNIECQTVEATDPLYILYTSGT 272

Query: 243 TGAPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTT 302
           TG PKGV+R   GH VAL W+MK+IY++DPGDVFWAASDVGWVVGHSYI YGPL+ G TT
Sbjct: 273 TGQPKGVVRDNGGHAVALAWSMKHIYDIDPGDVFWAASDVGWVVGHSYIVYGPLLVGATT 332

Query: 303 IVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTAIRAVKREDPKGEMLAKYDLSHLKALY 362
           ++FEGKPVGTPD G FWR I+++ VKSFFTAPTAIRA+KR+DP+G+ L   DLS L  L+
Sbjct: 333 VLFEGKPVGTPDPGIFWRTIAKYNVKSFFTAPTAIRAIKRDDPEGDYLKDVDLSCLGTLF 392

Query: 363 LAGERADPDTIIWAQKALSVPVIDHWWQTETGWTIAGNPLGIEELPTKLGSPAKAMPGYD 422
           LAGER DPDT+ WA++ L  PVIDHWWQTETGW +A N +G   +P K GSPAKA+PGYD
Sbjct: 393 LAGERCDPDTLHWAEQQLDKPVIDHWWQTETGWPVAANLMGTAPVPVKAGSPAKAVPGYD 452

Query: 423 VQILDEGGHQMKPGELGAIAVKLPLPPGTLPGLWNAEARFRKSYLEHFPGYYETGDAGMI 482
           VQ+LDE G  + P + G + +KLPLPPGTL  LW  E R+++SYL  +PGYY TGDAG +
Sbjct: 453 VQVLDEMGDVVAPDQSGNVVIKLPLPPGTLATLWQNEGRYKESYLSMYPGYYLTGDAGYM 512

Query: 483 DEDGYLYIMARTDDVINVAGHRLSTGGMEEVLAGHEDVAECAVIGVSDDLKGQMPLGFLC 542
           DEDGYLYIM+R DD+INVAGHRLSTG  EEVL  HE VAE AVIGV D LKGQ+PLG + 
Sbjct: 513 DEDGYLYIMSRIDDIINVAGHRLSTGRFEEVLCQHEAVAEAAVIGVDDKLKGQVPLGLVV 572

Query: 543 LNNGCNRDHGDVVKEVVKLVRDKIGPVAAFKLAVVVDRLPKTRSGKILRGTMVSIADGKE 602
           L  GC+     + KE++ LVR++IGPVAAFKL   V +LPKTRSGKILRGTM  IAD +E
Sbjct: 573 LKKGCDLSDEQLYKELIALVREQIGPVAAFKLVSAVPKLPKTRSGKILRGTMRKIADNQE 632

Query: 603 YKMPATIDDPAILDEIKVALQSLGYA 628
           +KMPATI+DP  L+ ++ AL  +GYA
Sbjct: 633 FKMPATIEDPYTLELVRNALTRMGYA 658


Lambda     K      H
   0.319    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: 1398
Number of extensions: 58
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: 662
Length adjustment: 38
Effective length of query: 591
Effective length of database: 624
Effective search space:   368784
Effective search space used:   368784
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis