GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Psychromonas ingrahamii 37

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 WP_041766327.1 PING_RS09720 acetate--CoA ligase

Query= SwissProt::Q9H6R3
         (686 letters)



>NCBI__GCF_000015285.1:WP_041766327.1
          Length = 629

 Score =  630 bits (1625), Expect = 0.0
 Identities = 304/627 (48%), Positives = 426/627 (67%), Gaps = 6/627 (0%)

Query: 60  SEYKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDR 119
           S Y+  F  +  DP  FW + A+ I W+K   K L    +    WF +G +N  Y A+D 
Sbjct: 4   SAYQNEFNRAKNDPLTFWQEQAKAIEWFKFPEKILSKDENGIDSWFADGQMNTAYLALDY 63

Query: 120 HIENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIP 179
           H+ NG+GD+ A+IYDSPV+  K  +TYKE+ + V++ AG+L   G+ KGD V+IYMPMI 
Sbjct: 64  HVLNGRGDQTALIYDSPVSGKKQQYTYKELTDHVARTAGMLADLGVVKGDRVIIYMPMIA 123

Query: 180 QAMYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVE 239
           +++  MLACAR+GA+HS++FGGFA  EL  RI+  +PKV++TAS GIE  + + Y+PL+ 
Sbjct: 124 ESVMAMLACARLGAVHSVVFGGFAPNELVIRIEDAEPKVIMTASCGIEVKKIIPYMPLIN 183

Query: 240 EALKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYT 299
           +A+   + KP  +++  R    A  L   RD+DW E++A +  HDCVPV    PLYILYT
Sbjct: 184 KAMADSRFKPKNVVVLQRDEYPA-ELTENRDIDWAEQVAISAPHDCVPVSGRDPLYILYT 242

Query: 300 SGTTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHG 359
           SGTTG PKGV+R  GG+AV L +SMS+IY  +PG+V+WAASD+GWVVGHSYI Y PL+HG
Sbjct: 243 SGTTGKPKGVVRENGGHAVALKYSMSTIYDAKPGDVYWAASDVGWVVGHSYIVYAPLIHG 302

Query: 360 NTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFK 419
            TT+LYEGKPV TPD GA++RV  E+ V  LF+APTA RAI+++DP   L KQY +   +
Sbjct: 303 CTTILYEGKPVRTPDPGAFWRVCEEYKVNILFSAPTAFRAIKKEDPEGELIKQYKMPDLR 362

Query: 420 TLFVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPP--PGQAGK 477
           T+F+AGER D  TLEW ++   +PV+DHWWQTETG  I+ + +GL   +T P  PG + K
Sbjct: 363 TIFMAGERLDPPTLEWVQSKTHLPVIDHWWQTETGWAISGNPLGL---ETFPLKPGSSTK 419

Query: 478 SVPGYNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDT 537
            VPG+ V ILD+  + L     G IV+K PLPPG  + +W++ E F+  Y  +FPGYY +
Sbjct: 420 PVPGFQVDILDEAGEPLPPNTQGYIVIKCPLPPGCLTTVWRHHERFQSGYLTQFPGYYVS 479

Query: 538 MDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHV 597
            D GY+D++GYL+VM R+DDVINVAGHR+S G +EE +  H  VA+CAV+G  D LKG +
Sbjct: 480 GDGGYIDDDGYLFVMGRIDDVINVAGHRLSTGEMEEVLGGHPDVAECAVIGAHDELKGQM 539

Query: 598 PLALCVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSA 657
           P+   VL+    + +  V +E+++ +R +IG VA+ +  + V +LPKTRSGK+ R  +  
Sbjct: 540 PIGFVVLKDGHYSVDGNVEKELIQKIRDDIGAVASLKRVLVVNRLPKTRSGKVLRRTIKQ 599

Query: 658 IVNGKPYKITSTIEDPSIFGHVEEMLK 684
           + +G+ Y + STI+DPS    +E  L+
Sbjct: 600 VADGEQYTMPSTIDDPSSITEIESALQ 626


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: 1274
Number of extensions: 64
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: 686
Length of database: 629
Length adjustment: 38
Effective length of query: 648
Effective length of database: 591
Effective search space:   382968
Effective search space used:   382968
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