GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Marinobacter adhaerens HP15

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 GFF2099 HP15_2053 PrpE protein

Query= SwissProt::Q9H6R3
         (686 letters)



>FitnessBrowser__Marino:GFF2099
          Length = 624

 Score =  636 bits (1641), Expect = 0.0
 Identities = 313/629 (49%), Positives = 425/629 (67%), Gaps = 10/629 (1%)

Query: 61  EYKTHFAASVTDPERFWGKAAEQISWYKP----WTKTLENKHSPSTRWFVEGMLNICYNA 116
           +Y + F  S+  P+ FW + AE+I W +P    W  T +N H    +WF +G LN C  A
Sbjct: 2   DYHSEFRRSIDKPDEFWREQAEKIDWIEPPKTIWQPT-DNGHG---QWFPDGTLNTCDVA 57

Query: 117 VDRHIENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMP 176
           +D +I  G+GD+ A+IYDSPVT+T+ ++TY E+ ++V++ AG L   GI KGD V+IYMP
Sbjct: 58  LDANIRAGRGDQKALIYDSPVTDTQRSYTYNELTDEVARFAGALKDRGITKGDRVIIYMP 117

Query: 177 MIPQAMYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVP 236
           MIP+A+  ML CARIGAIHS++FGGFA+ EL+ RID  KPK V+TAS GIE  R +EY P
Sbjct: 118 MIPEAVIAMLGCARIGAIHSVVFGGFAAHELAVRIDDAKPKAVITASCGIEVTRVIEYKP 177

Query: 237 LVEEALKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYI 296
           LV++A+    HKP+  ++Y R  ++A  L   RD DW+E M  A+  D VPV S  PLYI
Sbjct: 178 LVDKAIDQASHKPETCIVYQRQQVQA-ELQACRDHDWNELMETAEPADPVPVKSTDPLYI 236

Query: 297 LYTSGTTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPL 356
           LYTSGTTG PKGV+R  GG+AV L++SM  +Y  +PG+V+WAASD+GWVVGHSYI Y PL
Sbjct: 237 LYTSGTTGKPKGVVRDNGGHAVALNYSMKLVYDAKPGDVYWAASDVGWVVGHSYIVYAPL 296

Query: 357 LHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLT 416
             G TT++YEGKPV TPDAGA++RV+ +H V  LFTAPTA RA+R++DP A    +Y ++
Sbjct: 297 FAGCTTIMYEGKPVKTPDAGAFWRVVQDHKVNMLFTAPTAFRAVRKEDPEADQLSRYDIS 356

Query: 417 RFKTLFVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAG 476
             K LF+AGER D  T EW K    +PVLDHWWQTETG  I  + VG+    T  PG A 
Sbjct: 357 SLKRLFLAGERLDPATYEWLKEHTGLPVLDHWWQTETGWAICCNPVGIELMAT-KPGSAT 415

Query: 477 KSVPGYNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYD 536
              PGYNV ++D N  ++ A   G I VKLPLPPG    +W + E F+  Y E   G+Y 
Sbjct: 416 VPSPGYNVQVVDMNGSQMPAGEQGQIAVKLPLPPGCMMTVWGDDERFRKTYLEPISGFYS 475

Query: 537 TMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGH 596
           + D G++D++GY++VM R DDVINVAGHR+S G +EE + SH  +A+C VVG  D +KG 
Sbjct: 476 SGDGGFIDDDGYVFVMGRTDDVINVAGHRLSTGEMEEVVASHPAIAECCVVGAHDDMKGQ 535

Query: 597 VPLALCVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALS 656
           +P+ L +++       +++ +E+V+ VR  IG +A FR A+ V +LPKTRSGKI R  + 
Sbjct: 536 IPIGLVLIKDGATIDHDELEDELVEMVRDKIGAIACFRRALVVDRLPKTRSGKILRRVIR 595

Query: 657 AIVNGKPYKITSTIEDPSIFGHVEEMLKQ 685
            I +G+ Y + STI+DP+I   + E  ++
Sbjct: 596 QIADGEEYSVPSTIDDPAILEEISEQFRR 624


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: 1175
Number of extensions: 44
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: 624
Length adjustment: 38
Effective length of query: 648
Effective length of database: 586
Effective search space:   379728
Effective search space used:   379728
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