Aligments for a candidate for acs in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Aligments 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources