Alignments for a candidate for acs in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Azospirillum brasilense Sp245

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

Query= BRENDA::A0A0G2K047
         (683 letters)



>FitnessBrowser__azobra:AZOBR_RS06340
          Length = 640

 Score =  708 bits (1827), Expect = 0.0
 Identities = 333/630 (52%), Positives = 451/630 (71%), Gaps = 2/630 (0%)

Query: 51  TSSGGGEYKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICY 110
           + S    Y    A S++DP+ FWG+AAE I+W K W K L++   P   WF  G+LN CY
Sbjct: 2   SQSSADRYNQIHARSLSDPDGFWGEAAEDITWIKRWDKVLDDSNAPFYRWFTGGVLNTCY 61

Query: 111 NAIDRHIENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIY 170
           NA+DRH+E G+G + AIIYDSPVT T  TI+Y E  +QV++ AG L  QGV+KGD V++Y
Sbjct: 62  NAVDRHVEAGRGAQAAIIYDSPVTKTVQTITYAEFQDQVARFAGALRAQGVEKGDRVILY 121

Query: 171 MPMIPQAIYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEY 230
           MPMIPQ++ AMLACAR+GA+HS++FGGFA  EL+TRI+  +PK +V+AS GIEP R V+Y
Sbjct: 122 MPMIPQSLVAMLACARLGAVHSVVFGGFAPHELATRINDSRPKAIVSASCGIEPNRVVKY 181

Query: 231 MPLLEEALRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPL 290
            P+L+ A+   +HKP  ++++ RP  E   L+ GRD+DW E +AKA+  +CVPV +  PL
Sbjct: 182 KPMLDAAIEQAEHKPSSVIVFQRPQ-ETATLVEGRDVDWAEAVAKAEPAECVPVAATDPL 240

Query: 291 YILYTSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYG 350
           YILYTSGTTG PKGV+R  GG+AV L WTM +IY ++PGEV+WAASD+GWVVGHSYI YG
Sbjct: 241 YILYTSGTTGQPKGVIRDNGGHAVALKWTMKNIYNVEPGEVYWAASDVGWVVGHSYIVYG 300

Query: 351 PLLHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYS 410
           PLLHG TTV++EGKPVGTPDAG ++RV+ +H +  LFTAPTA RAI+++DP A L K+Y 
Sbjct: 301 PLLHGCTTVVFEGKPVGTPDAGTFWRVIEQHKIGTLFTAPTAFRAIKREDPNAELLKKYD 360

Query: 411 LTRFKTLFVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQ 470
           L+ F+ LF+AGER D +TL W++    VPV+DHWWQTETG  I+ + +G+ +      G 
Sbjct: 361 LSHFRALFLAGERSDPDTLHWAEDNLNVPVIDHWWQTETGWAISGNPLGV-HLFPIKYGS 419

Query: 471 AGKCVPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGY 530
           A + +PG++V IL+   +++    +G I VKLPLPPG    LW   + ++  Y   +PGY
Sbjct: 420 ATRPMPGWDVQILNAENKEVPRGDIGAICVKLPLPPGTLPTLWNADDRYRKSYLSDYPGY 479

Query: 531 YDTMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLK 590
           Y T DAG++D++GY+Y+M+R DD+INVAGHR+S G +EE + SH  V +CAV+G  D LK
Sbjct: 480 YQTGDAGFIDDDGYVYIMARTDDIINVAGHRLSTGGMEEVLASHKDVAECAVIGVADDLK 539

Query: 591 GHVPLALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRST 650
           G VPL    LK  V    E++++E+V+ VR+ IGPVA F+ AV V++LPKTRSGKI R T
Sbjct: 540 GQVPLGFLCLKAGVTRPHEEIVKEVVQLVREQIGPVADFKRAVVVERLPKTRSGKILRGT 599

Query: 651 LSALVNGKPYKVTPTIEDPSIFGHIEEVLK 680
           +  + + + YK   TI+DP I   I E L+
Sbjct: 600 MQKIADNQDYKTPATIDDPGILPEIAEALQ 629


Lambda     K      H
   0.318    0.136    0.421 

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: 1333
Number of extensions: 49
Number of successful extensions: 3
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: 683
Length of database: 640
Length adjustment: 38
Effective length of query: 645
Effective length of database: 602
Effective search space:   388290
Effective search space used:   388290
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