GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Microvirga lotononidis WSM3557

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_009763407.1 MICLODRAFT_RS18895 propionyl-CoA synthetase

Query= BRENDA::A0A0G2K047
         (683 letters)



>NCBI__GCF_000262405.1:WP_009763407.1
          Length = 637

 Score =  682 bits (1760), Expect = 0.0
 Identities = 330/627 (52%), Positives = 439/627 (70%), Gaps = 7/627 (1%)

Query: 58  YKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHI 117
           Y   +A  +ADP  FW +AA +I W +P     +        WFV    N CYNA+DRH+
Sbjct: 8   YHEVYAGWMADPAGFWERAAREIDWIRPAETVFDRDAGIYGRWFVGAECNTCYNAVDRHV 67

Query: 118 ENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQA 177
              +G + AIIYDSPVT TK +I+Y E+ ++V+ LA VL   GV KGD VVIYMPMIP+ 
Sbjct: 68  AT-RGGQAAIIYDSPVTGTKRSITYAELRDEVATLAAVLQDMGVTKGDRVVIYMPMIPET 126

Query: 178 IYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEA 237
            +AMLACARIGAIHS++FGGFA+KEL+TRID  KPKV+++AS GIE  R + Y PLL+EA
Sbjct: 127 SFAMLACARIGAIHSVVFGGFAAKELATRIDDAKPKVILSASCGIEGARVIPYKPLLDEA 186

Query: 238 LRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHD----CVPVLSEHPLYIL 293
           + +   KP+  L++ RP +    L+ GRD DW + +A+A+  D    CVPV +  PLY+L
Sbjct: 187 IALSSFKPEACLVFQRPQLA-CALVEGRDRDWADAVAEAKVEDRRAECVPVAATDPLYVL 245

Query: 294 YTSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLL 353
           YTSGTTG+PKGVVR  GG+ V L W+M   +G+KPGEV+WAASD+GWVVGHSYI YGPLL
Sbjct: 246 YTSGTTGIPKGVVRDNGGHMVALKWSMEHFFGVKPGEVFWAASDVGWVVGHSYIVYGPLL 305

Query: 354 HGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTR 413
           HG T VLYEGKPVGTPDAGAY+RV+++HGV  LFTAPTA RAI+++DP A L ++Y L+ 
Sbjct: 306 HGCTAVLYEGKPVGTPDAGAYWRVISDHGVVTLFTAPTAFRAIKKEDPKAELLRKYDLSS 365

Query: 414 FKTLFVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGK 473
           F+ LF+AGER D +T++W++ + +VPV+DHWWQTETG P+  + +GLG +     G    
Sbjct: 366 FRALFLAGERADPDTVKWAEDILQVPVIDHWWQTETGWPVAGNPLGLG-ALPVKHGSPTV 424

Query: 474 CVPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDT 533
            +PGY + +LD+  + +   ++G IV+KLPLPPGA   LW+  E F+  Y   +PGYY+T
Sbjct: 425 PMPGYVLEVLDEGGKPVAPNTMGAIVIKLPLPPGALPTLWQADERFRESYLSVYPGYYNT 484

Query: 534 MDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHV 593
            DAGY+DE+GY++VM R DD+INVAGHR+S G +EE + SH  V +CAV+G +D LKG V
Sbjct: 485 SDAGYLDEDGYIWVMGRTDDIINVAGHRLSTGGMEEVLASHPAVAECAVIGVKDALKGEV 544

Query: 594 PLALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSA 653
           P    VLK  ++   E +  E+V  VR  IGPVAAF+ A+ V +LPKTRSGKI R T+  
Sbjct: 545 PCGFVVLKSGIDRPPETIEAELVALVRDRIGPVAAFKLAITVARLPKTRSGKILRGTMKK 604

Query: 654 LVNGKPYKVTPTIEDPSIFGHIEEVLK 680
           + +G  +    TI+DP I   I + L+
Sbjct: 605 IADGDTWSTPATIDDPMILSEIGDALR 631


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: 1376
Number of extensions: 76
Number of successful extensions: 6
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: 637
Length adjustment: 38
Effective length of query: 645
Effective length of database: 599
Effective search space:   386355
Effective search space used:   386355
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