Alignments for a candidate for acs in Marinobacter guineae M3B

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Marinobacter guineae M3B

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_099617596.1 CLH62_RS02220 propionyl-CoA synthetase

Query= SwissProt::Q9H6R3
         (686 letters)



>NCBI__GCF_002744735.1:WP_099617596.1
          Length = 624

 Score =  644 bits (1662), Expect = 0.0
 Identities = 316/628 (50%), Positives = 428/628 (68%), Gaps = 10/628 (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   DYHSEFRRSIDNPDDFWREQAEKIDWIEPPKTIWQPT-DNGHG---QWFPDGTLNTCDVA 57

Query: 117 VDRHIENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMP 176
           +D +I  G+GD+ A+IYDSPVTNTK ++TY E+ ++V++ AGVL   GI KGD V+IYMP
Sbjct: 58  LDANIRAGRGDQKALIYDSPVTNTKRSYTYSELTDEVARFAGVLKGRGITKGDRVIIYMP 117

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

Query: 237 LVEEALKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYI 296
           LV +A+    HKP+  ++Y RP  +A  L  GRD DW+E MA A+    VPV S  PLYI
Sbjct: 178 LVNKAIDQASHKPETCIVYQRPQAKA-DLIQGRDFDWNELMAAAEPAAPVPVKSTDPLYI 236

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

Query: 357 LHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLT 416
             G T++LYEGKPV TPDAGA++RV+ +H V  LFTAPTA RA+R++DP A    +Y+++
Sbjct: 297 FAGCTSILYEGKPVKTPDAGAFWRVVQDHKVNMLFTAPTAFRAVRKEDPEADQLSRYNIS 356

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

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

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

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

Query: 657 AIVNGKPYKITSTIEDPSIFGHVEEMLK 684
            I +G+ Y + STI+DP+I   + E  +
Sbjct: 596 QIADGEEYAVPSTIDDPAILEEISEQFR 623


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: 1178
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 24 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
the source code
instructions for running GapMind on your computer

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