GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Shewanella halifaxensis HAW-EB4

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_012277976.1 SHAL_RS15005 propionyl-CoA synthetase

Query= BRENDA::A0A0G2K047
         (683 letters)



>NCBI__GCF_000019185.1:WP_012277976.1
          Length = 634

 Score =  672 bits (1735), Expect = 0.0
 Identities = 322/617 (52%), Positives = 431/617 (69%), Gaps = 2/617 (0%)

Query: 63  AASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHIENGQG 122
           A S+  PE FW +AA QI W+ PW   L++   P   WF  G LN CYNA+DRH++ G+G
Sbjct: 10  AKSINQPEAFWAEAASQIDWFSPWNNVLDDSEAPFYHWFKGGKLNTCYNAVDRHVDAGRG 69

Query: 123 DKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQAIYAML 182
           D+IA+ Y SPVTD +  ISY+E+L QVS+LAG +   GVKKGD VVIYMPM+P+  +AML
Sbjct: 70  DQIALQYVSPVTDVEYGISYRELLAQVSRLAGYMDSIGVKKGDRVVIYMPMVPETAFAML 129

Query: 183 ACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEALRIGQ 242
           ACARIGAIHS++FGGFA+ EL+TRI+  KPK++++AS GIEP   + Y PLL+ AL    
Sbjct: 130 ACARIGAIHSVVFGGFAANELATRINDAKPKLILSASCGIEPSGIIPYKPLLDAALDQAT 189

Query: 243 HKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLP 302
           HK D  L+ NR  +E   L  GRD+DW+  +A A + DC P+ +  PLYILYTSGTTG P
Sbjct: 190 HKVDHCLVLNRGQLE-AELFPGRDIDWQAAVAAAPNIDCQPLDATDPLYILYTSGTTGQP 248

Query: 303 KGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYE 362
           KGVVR  GG+AV L W+M  IY +  G+V+WAASD+GWVVGHSYI YGPLL G T++LYE
Sbjct: 249 KGVVRDNGGHAVALAWSMKHIYDINAGDVFWAASDVGWVVGHSYIVYGPLLVGATSILYE 308

Query: 363 GKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAGE 422
           GKP+GTPD GA++R +A++ V + FTAPTAIRAI++ DP     +   L+  K +F+AGE
Sbjct: 309 GKPIGTPDPGAFWRTIAKYRVKSFFTAPTAIRAIKRDDPHGDYLEGVDLSCLKNVFLAGE 368

Query: 423 RCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGKCVPGYNVMI 482
           RCD +TL W++   + PV+DHWWQTETG P+ A+ +G    +    G     VPGY + +
Sbjct: 369 RCDPDTLHWTEGKLKKPVIDHWWQTETGWPVAANLMGYAPVEI-KAGSPALAVPGYQIEV 427

Query: 483 LDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDEE 542
           +D    +++A   GN+V+KLPLPPG  + LW+N++ ++  Y   +PGYY T DAGY DE+
Sbjct: 428 VDVMGDEVEANESGNVVIKLPLPPGTLTTLWQNEQRYQDSYLSMYPGYYLTGDAGYKDED 487

Query: 543 GYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLALCVLKK 602
           GYLY+MSR+DD+INVAGHR+S G  EE +  H  V + AV+G +D LKG VPL L VLKK
Sbjct: 488 GYLYIMSRIDDIINVAGHRLSTGRFEEVLCQHEAVAEAAVIGVKDVLKGQVPLGLVVLKK 547

Query: 603 DVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNGKPYKV 662
            V+  ++ + ++++  VRQ IGPVA+FR    V++LPKTRSGKI R T+  + + + Y V
Sbjct: 548 GVSLNDDDLNQQLMSLVRQEIGPVASFRLVSAVQKLPKTRSGKILRGTMRNIADNQSYNV 607

Query: 663 TPTIEDPSIFGHIEEVL 679
             TIEDP+    +   L
Sbjct: 608 PATIEDPATLDIVRNTL 624


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: 1276
Number of extensions: 59
Number of successful extensions: 4
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: 634
Length adjustment: 38
Effective length of query: 645
Effective length of database: 596
Effective search space:   384420
Effective search space used:   384420
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.

Links

Downloads

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:

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