Alignments for a candidate for prpE in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Azospirillum brasilense Sp245

Align propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate AZOBR_RS06340 AZOBR_RS06340 acyl-CoA synthetase

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



>FitnessBrowser__azobra:AZOBR_RS06340
          Length = 640

 Score =  930 bits (2403), Expect = 0.0
 Identities = 439/627 (70%), Positives = 515/627 (82%)

Query: 3   YQDVYESWKSDPEAFWMEAAKSIDWVEAPSRALDDSNAPLYEWFTDAKVNTCWNAVDRHV 62
           Y  ++    SDP+ FW EAA+ I W++   + LDDSNAP Y WFT   +NTC+NAVDRHV
Sbjct: 9   YNQIHARSLSDPDGFWGEAAEDITWIKRWDKVLDDSNAPFYRWFTGGVLNTCYNAVDRHV 68

Query: 63  EAGRGEQTAIIYDSPITHTKRQISYVELRNRVAMLAGALRAKGVEKGDRVIIYMPMIPEA 122
           EAGRG Q AIIYDSP+T T + I+Y E +++VA  AGALRA+GVEKGDRVI+YMPMIP++
Sbjct: 69  EAGRGAQAAIIYDSPVTKTVQTITYAEFQDQVARFAGALRAQGVEKGDRVILYMPMIPQS 128

Query: 123 LEAMLACARLGAVHSVVFGGFAANELAVRIDDAQPKAIIAASCGLEPGRVVHYKPLLDGA 182
           L AMLACARLGAVHSVVFGGFA +ELA RI+D++PKAI++ASCG+EP RVV YKP+LD A
Sbjct: 129 LVAMLACARLGAVHSVVFGGFAPHELATRINDSRPKAIVSASCGIEPNRVVKYKPMLDAA 188

Query: 183 IDMAKHKPEFCVIFQREQEVAHLEEGRDYNWHGFQYGVEPAECVPVEGNHPAYILYTSGT 242
           I+ A+HKP   ++FQR QE A L EGRD +W       EPAECVPV    P YILYTSGT
Sbjct: 189 IEQAEHKPSSVIVFQRPQETATLVEGRDVDWAEAVAKAEPAECVPVAATDPLYILYTSGT 248

Query: 243 TGAPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTT 302
           TG PKGV+R   GH VAL WTMKNIYNV+PG+V+WAASDVGWVVGHSYI YGPL+HG TT
Sbjct: 249 TGQPKGVIRDNGGHAVALKWTMKNIYNVEPGEVYWAASDVGWVVGHSYIVYGPLLHGCTT 308

Query: 303 IVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTAIRAVKREDPKGEMLAKYDLSHLKALY 362
           +VFEGKPVGTPDAGTFWRVI +HK+ + FTAPTA RA+KREDP  E+L KYDLSH +AL+
Sbjct: 309 VVFEGKPVGTPDAGTFWRVIEQHKIGTLFTAPTAFRAIKREDPNAELLKKYDLSHFRALF 368

Query: 363 LAGERADPDTIIWAQKALSVPVIDHWWQTETGWTIAGNPLGIEELPTKLGSPAKAMPGYD 422
           LAGER+DPDT+ WA+  L+VPVIDHWWQTETGW I+GNPLG+   P K GS  + MPG+D
Sbjct: 369 LAGERSDPDTLHWAEDNLNVPVIDHWWQTETGWAISGNPLGVHLFPIKYGSATRPMPGWD 428

Query: 423 VQILDEGGHQMKPGELGAIAVKLPLPPGTLPGLWNAEARFRKSYLEHFPGYYETGDAGMI 482
           VQIL+    ++  G++GAI VKLPLPPGTLP LWNA+ R+RKSYL  +PGYY+TGDAG I
Sbjct: 429 VQILNAENKEVPRGDIGAICVKLPLPPGTLPTLWNADDRYRKSYLSDYPGYYQTGDAGFI 488

Query: 483 DEDGYLYIMARTDDVINVAGHRLSTGGMEEVLAGHEDVAECAVIGVSDDLKGQMPLGFLC 542
           D+DGY+YIMARTDD+INVAGHRLSTGGMEEVLA H+DVAECAVIGV+DDLKGQ+PLGFLC
Sbjct: 489 DDDGYVYIMARTDDIINVAGHRLSTGGMEEVLASHKDVAECAVIGVADDLKGQVPLGFLC 548

Query: 543 LNNGCNRDHGDVVKEVVKLVRDKIGPVAAFKLAVVVDRLPKTRSGKILRGTMVSIADGKE 602
           L  G  R H ++VKEVV+LVR++IGPVA FK AVVV+RLPKTRSGKILRGTM  IAD ++
Sbjct: 549 LKAGVTRPHEEIVKEVVQLVREQIGPVADFKRAVVVERLPKTRSGKILRGTMQKIADNQD 608

Query: 603 YKMPATIDDPAILDEIKVALQSLGYAK 629
           YK PATIDDP IL EI  ALQSLGYAK
Sbjct: 609 YKTPATIDDPGILPEIAEALQSLGYAK 635


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: 1433
Number of extensions: 55
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 ( 7.4 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.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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
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