GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Shewanella amazonensis SB2B

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 6937194 Sama_1364 acyl-coenzyme A synthetase/AMP-(fatty) acid ligase (RefSeq)

Query= SwissProt::Q9H6R3
         (686 letters)



>FitnessBrowser__SB2B:6937194
          Length = 644

 Score =  660 bits (1702), Expect = 0.0
 Identities = 315/612 (51%), Positives = 425/612 (69%), Gaps = 2/612 (0%)

Query: 72  DPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHIENGKGDKIAI 131
           +PE++W KAA+ + W+K  +  L++  +P  RW+ +G +N CYNA+DR ++ G+G + A 
Sbjct: 25  NPEQYWRKAADMVDWHKAPSTILDSSQAPLYRWYTDGEINTCYNALDRQVDAGRGSQTAF 84

Query: 132 IYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQAMYTMLACARI 191
            Y SPVT T+ + +Y E L QV +LAG+L   G+ KGD VVIYMPM+P+  Y MLACARI
Sbjct: 85  HYVSPVTETEYSISYTECLAQVKRLAGLLKAQGVNKGDRVVIYMPMVPETAYAMLACARI 144

Query: 192 GAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEALKIGQHKPDK 251
           GAIHS++FGGFA+ EL+SRI+  KP +V++AS G+EP   V Y PL++ AL    HK  K
Sbjct: 145 GAIHSVVFGGFAANELASRINDAKPVMVLSASCGVEPSGVVAYKPLLDAALAQASHKVSK 204

Query: 252 ILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLPKGVIR 311
            LI  RP  EA  + PGRDLDW E +A A   D VPV +  PLY+LYTSGTTG PKGV+R
Sbjct: 205 CLILQRPQYEAA-MTPGRDLDWQESVASAADADWVPVKATDPLYVLYTSGTTGQPKGVVR 263

Query: 312 PTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYEGKPVG 371
             GG+AV L WSM  +Y ++PG+ +WAASD+GWVVGHSYI YGPL+ G T+VLYEGKPVG
Sbjct: 264 DNGGHAVALAWSMRYLYDIEPGDTFWAASDVGWVVGHSYIVYGPLIAGATSVLYEGKPVG 323

Query: 372 TPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAGERCDVE 431
           TPDAGA++R + ++GV + FTAPTAIRAI+++DP     +  +L   K +F+AGERCD +
Sbjct: 324 TPDAGAFWRTIKKYGVKSFFTAPTAIRAIKREDPEGFFCRNTNLDCLKQMFLAGERCDPD 383

Query: 432 TLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAGKSVPGYNVMILDDNM 491
           TL W++ +   PV+DHWWQTETG P+ ++ +G+       PG   + VPGY V ++D+  
Sbjct: 384 TLLWAQEMLGKPVIDHWWQTETGWPVASNLMGIAQMPI-KPGSPARPVPGYQVDVVDEAG 442

Query: 492 QKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDEEGYLYV 551
             + A   GN+V++LPLPPG    LW+N + +   Y   +P  Y T DAGYMDE+GYLY+
Sbjct: 443 NSVGAGEYGNVVIRLPLPPGTLPTLWQNDKRYIDSYLSMYPDCYLTGDAGYMDEDGYLYI 502

Query: 552 MSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHVPLALCVLRKDINAT 611
           MSR+DDVINVAGHR+S G  EE +  H  VA+ AV+G ED LKG VPL L VL+  ++ T
Sbjct: 503 MSRIDDVINVAGHRLSTGRFEEVLCQHPAVAEAAVIGVEDKLKGQVPLGLVVLKNGVDIT 562

Query: 612 EEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSAIVNGKPYKITSTIE 671
           +EQ+ +E+V  VR  IGPVAAF+    + +LPKTRSGKI R+ +  I + + Y + +TIE
Sbjct: 563 DEQLNKELVALVRSEIGPVAAFKLVSAIPKLPKTRSGKILRATMRKIADNQEYSVPATIE 622

Query: 672 DPSIFGHVEEML 683
           DP+    V   L
Sbjct: 623 DPATLELVRNTL 634


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: 1250
Number of extensions: 60
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 686
Length of database: 644
Length adjustment: 38
Effective length of query: 648
Effective length of database: 606
Effective search space:   392688
Effective search space used:   392688
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