GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Cupriavidus basilensis 4G11

Align Acyl-CoA synthetase short-chain family member 3, mitochondrial; Acetate--CoA ligase 3; Acyl-CoA synthetase short-chain family member 3; Propionate--CoA ligase; EC 6.2.1.1; EC 6.2.1.17 (characterized)
to candidate RR42_RS13560 RR42_RS13560 propionyl-CoA synthetase

Query= SwissProt::Q9H6R3
         (686 letters)



>FitnessBrowser__Cup4G11:RR42_RS13560
          Length = 630

 Score =  510 bits (1314), Expect = e-149
 Identities = 279/634 (44%), Positives = 395/634 (62%), Gaps = 29/634 (4%)

Query: 67  AASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHIENGKG 126
           A S++DPE FW + A +I W  P+   L++   P TRWFV G  N+C+NAVDRH+   + 
Sbjct: 9   ARSLSDPEGFWAEQARRIDWETPFDTVLDDSRPPFTRWFVGGRTNLCHNAVDRHLAE-RA 67

Query: 127 DKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQAMYTML 186
           D+ A+IY S  T    T++Y E+ ++V+++A +L + G+ KGD V+IYMPMIP+A + ML
Sbjct: 68  DQAALIYVSTETGQHRTYSYAELHDEVNRMAAILQQLGVVKGDRVLIYMPMIPEAAFAML 127

Query: 187 ACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEALKIGQ 246
           ACARIGAIHS++FGGFAS  L++RID  +P+V+V+A  G   G+ V Y PL++EA+K+  
Sbjct: 128 ACARIGAIHSVVFGGFASVSLAARIDDAQPRVIVSADAGSRAGKVVPYKPLLDEAVKLAT 187

Query: 247 HKPDKILIYNRPNMEAVPLAPGRDLD---WDEEMAKAQSHDCVPVLSEHPLYILYTSGTT 303
           HKP+++L+ +R  +  + L PGRD D   W E +  A+   C  + S  P Y+LYTSGTT
Sbjct: 188 HKPERVLLVDR-QLSPMTLTPGRDEDYGAWRERVGAARV-PCAWLESSEPSYVLYTSGTT 245

Query: 304 GLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGNTTV 363
           G PKGV R TGGYAV L  SM  I+  + G+  +++SD+GWVVGHSYI YGPLL G  T+
Sbjct: 246 GKPKGVQRDTGGYAVALAASMEYIFCGKAGDTMFSSSDIGWVVGHSYIIYGPLLAGMATI 305

Query: 364 LYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFV 423
           +YEG P+  PD G  ++++ ++ V  +F+APTAIR +++QDP  A   +Y L+  + LF+
Sbjct: 306 MYEGTPI-RPDGGILWQLVEQYHVNIMFSAPTAIRVLKKQDP--AWLTRYDLSSLRLLFL 362

Query: 424 AGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPP---GQAGKSVP 480
           AGE  D  T  W +     PV+D++WQTETG PI A   GL     P P   G  G  V 
Sbjct: 363 AGEPLDEPTASWIQQGIGKPVVDNYWQTETGWPIIAIQRGL----DPLPAKLGSPGVPVY 418

Query: 481 GYNVMILDDNMQKLKARC----LGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPG--Y 534
           GY++ I+D   +   A C     G + +  PLPPG  + +W + E F   Y+   PG   
Sbjct: 419 GYDLKIID---EATGAECPPGQKGVVAIDGPLPPGCMTTVWGDDERFVKTYWSGVPGRRC 475

Query: 535 YDTMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLK 594
           Y T D G  DE+GY++++ R DDVINVAGHR+    IEESI SH  VA+ AVVG  D LK
Sbjct: 476 YSTFDWGVQDEDGYIFILGRTDDVINVAGHRLGTREIEESISSHPAVAEVAVVGVHDALK 535

Query: 595 GHVPLALCVLR---KDINATEEQVLE-EIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKI 650
           G   +A  ++R   +     +  VLE +++K V Q +G VA      FV  LPKTRSGK+
Sbjct: 536 GQAAMAFVIVRDAGRTATQADRLVLEGDVMKTVDQQLGAVARPARVFFVNALPKTRSGKL 595

Query: 651 PRSALSAIVNGKPYKITSTIEDPSIFGHVEEMLK 684
            R A+ A+  G+     +TIEDP+    ++  ++
Sbjct: 596 LRRAMQAVAEGRDPGDLTTIEDPTALAQLQAAMQ 629


Lambda     K      H
   0.318    0.136    0.422 

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: 1130
Number of extensions: 61
Number of successful extensions: 8
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: 686
Length of database: 630
Length adjustment: 38
Effective length of query: 648
Effective length of database: 592
Effective search space:   383616
Effective search space used:   383616
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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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