GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Brevibacterium jeotgali SJ5-8

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_101589101.1 BJEO58_RS08245 acetate--CoA ligase

Query= BRENDA::A0A0G2K047
         (683 letters)



>NCBI__GCF_900169175.1:WP_101589101.1
          Length = 645

 Score =  587 bits (1513), Expect = e-172
 Identities = 301/645 (46%), Positives = 415/645 (64%), Gaps = 18/645 (2%)

Query: 50  TTSSGGGEYKTHFAA----SVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGM 105
           +TS+   E    +AA    +  DP  FW  AA+ I W  P ++ L++   P   WF +G 
Sbjct: 3   STSAAHDEAPRTYAAVARSAADDPASFWLGAAQAIDWVTPPSRALDDANAPIYRWFPDGT 62

Query: 106 LNICYNAIDRHIENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGD 165
           LN+C NA+DRH+E G GD++A++YDSPVTDT    ++  + ++VS+ A  L  +G+ KGD
Sbjct: 63  LNVCANALDRHVEMGSGDRVALVYDSPVTDTVREYTFTALRDEVSRFARALADRGITKGD 122

Query: 166 TVVIYMPMIPQAIYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPG 225
            VVIYMPM+P+A  AMLACAR+GA+HS++FGGFA+ EL+ RID ++PK V+++S GIE  
Sbjct: 123 RVVIYMPMVPEATIAMLACARLGAVHSVVFGGFAANELAVRIDDLQPKAVISSSCGIEKT 182

Query: 226 RKVEYMPLLEEALRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKA-QSHDCVPV 284
           R +EY PLL+EALRI    P+  ++  R    +  L  G DLD+ + +A      D V V
Sbjct: 183 RIIEYKPLLDEALRIATAGPEFSVVVQR-EQHRAELQEGFDLDYADLLASTPDGIDPVTV 241

Query: 285 LSEHPLYILYTSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGH 344
            +  PLY+LYTSGTTG PKG++R  GGYAV L W+M +++GL+PG+  + ASD+GWVVGH
Sbjct: 242 QATDPLYVLYTSGTTGRPKGILRDAGGYAVALQWSMGNLFGLQPGDTMFTASDVGWVVGH 301

Query: 345 SYICYGPLLHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAA 404
           SYI Y PLL G TTVLYEGKPVGTPDA A++RV+ +H V   FTAPTA+R IR++DP A 
Sbjct: 302 SYIVYAPLLAGVTTVLYEGKPVGTPDASAFYRVMDQHDVNVFFTAPTAMRVIRKEDPDAE 361

Query: 405 LGKQYSLTRFKTLFVAGERCDVETLEWSKKVFR------VPVLDHWWQTETGSPITASCI 458
             +   L+  + +F+AGER D +T EW+           +PV+D+WWQTETG PI A+ +
Sbjct: 362 HARAADLSALRAVFLAGERLDPDTYEWTTATMAEATGRDIPVVDNWWQTETGWPIAANPL 421

Query: 459 GLGNSKTP-PPGQAGKCVPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQE 517
           G+   + P   G      PGY + ++D     ++A + G I+  LPLPPG  + +W + E
Sbjct: 422 GI--ERLPLKAGSPTVPTPGYRLRVVDPAGNDVRAGTEGLILADLPLPPGTMASIWGDDE 479

Query: 518 AFKHLYFEKFPGYYDTMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTV 577
            F   Y   F G Y T D+GY+DE+GY++VM R DDVINV+GHR+S G +E ++ SH  V
Sbjct: 480 RFVSTYLSTFEGTYLTGDSGYLDEDGYVFVMGRTDDVINVSGHRLSTGVLEAAIASHPAV 539

Query: 578 TDCAVVGKEDPLKGHVPLALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQ 637
           T+CAV+G  D   G  P A  VL    +A  E V +E+V  VR+ +GPVAA R    V  
Sbjct: 540 TECAVIGVHDETSGQSPRAFVVLSP--SADPEMVPQELVALVRREVGPVAALRRVDVVDA 597

Query: 638 LPKTRSGKIPRSTLSALVNGKPYKVTP-TIEDPSIFGHIEEVLKQ 681
           LPKTRSGKI R T+  + +G+   V P TIEDPS+   +   L +
Sbjct: 598 LPKTRSGKILRKTMRQISDGEADVVVPSTIEDPSVLDAMRTALSR 642


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: 1184
Number of extensions: 59
Number of successful extensions: 5
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: 645
Length adjustment: 38
Effective length of query: 645
Effective length of database: 607
Effective search space:   391515
Effective search space used:   391515
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 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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