GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Shewanella loihica PV-4

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate 5210124 Shew_2568 AMP-dependent synthetase and ligase (RefSeq)

Query= BRENDA::A0A0G2K047
         (683 letters)



>FitnessBrowser__PV4:5210124
          Length = 662

 Score =  673 bits (1736), Expect = 0.0
 Identities = 323/608 (53%), Positives = 432/608 (71%), Gaps = 8/608 (1%)

Query: 65  SVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHIENGQGDK 124
           S+ +P  FWG+AA  ++W K + + L++   P   WF  G LN CYNA+DRH+E G+G++
Sbjct: 40  SIDNPNAFWGEAAGALAWDKTFERVLDDSQAPMYRWFSGGQLNTCYNAVDRHVEAGRGEQ 99

Query: 125 IAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQAIYAMLAC 184
           +AI Y SP+T T+  I+Y E+  QVS+LAG +  QGV KGD V+IYMPM+P+  YAMLAC
Sbjct: 100 VAIQYVSPITGTEYGITYNELQAQVSRLAGYMASQGVVKGDRVIIYMPMVPETAYAMLAC 159

Query: 185 ARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEALRIGQHK 244
           AR+GAIHS++FGGFA+ EL+TRID   PK++++AS G+EP   V Y PLL++AL    HK
Sbjct: 160 ARLGAIHSVVFGGFAANELATRIDDATPKMILSASCGVEPSGVVAYKPLLDDALEQASHK 219

Query: 245 PDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLPKG 304
            ++ +I NRP ++   L+ GRD+DW+  MA A + +C  V +  PLYILYTSGTTG PKG
Sbjct: 220 VEQCVILNRPQLQ-ADLVDGRDVDWQGAMADAPNIECQTVEATDPLYILYTSGTTGQPKG 278

Query: 305 VVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYEGK 364
           VVR  GG+AV L W+M  IY + PG+V+WAASD+GWVVGHSYI YGPLL G TTVL+EGK
Sbjct: 279 VVRDNGGHAVALAWSMKHIYDIDPGDVFWAASDVGWVVGHSYIVYGPLLVGATTVLFEGK 338

Query: 365 PVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAGERC 424
           PVGTPD G ++R +A++ V + FTAPTAIRAI++ DP     K   L+   TLF+AGERC
Sbjct: 339 PVGTPDPGIFWRTIAKYNVKSFFTAPTAIRAIKRDDPEGDYLKDVDLSCLGTLFLAGERC 398

Query: 425 DVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAG---KCVPGYNVM 481
           D +TL W+++    PV+DHWWQTETG P+ A+ +G      P P +AG   K VPGY+V 
Sbjct: 399 DPDTLHWAEQQLDKPVIDHWWQTETGWPVAANLMG----TAPVPVKAGSPAKAVPGYDVQ 454

Query: 482 ILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDE 541
           +LD+    +     GN+V+KLPLPPG  + LW+N+  +K  Y   +PGYY T DAGYMDE
Sbjct: 455 VLDEMGDVVAPDQSGNVVIKLPLPPGTLATLWQNEGRYKESYLSMYPGYYLTGDAGYMDE 514

Query: 542 EGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLALCVLK 601
           +GYLY+MSR+DD+INVAGHR+S G  EE +  H  V + AV+G +D LKG VPL L VLK
Sbjct: 515 DGYLYIMSRIDDIINVAGHRLSTGRFEEVLCQHEAVAEAAVIGVDDKLKGQVPLGLVVLK 574

Query: 602 KDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNGKPYK 661
           K  + ++EQ+ +E++  VR+ IGPVAAF+    V +LPKTRSGKI R T+  + + + +K
Sbjct: 575 KGCDLSDEQLYKELIALVREQIGPVAAFKLVSAVPKLPKTRSGKILRGTMRKIADNQEFK 634

Query: 662 VTPTIEDP 669
           +  TIEDP
Sbjct: 635 MPATIEDP 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: 1348
Number of extensions: 54
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: 683
Length of database: 662
Length adjustment: 39
Effective length of query: 644
Effective length of database: 623
Effective search space:   401212
Effective search space used:   401212
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