GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Algiphilus aromaticivorans DG1253

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_043768476.1 U743_RS11510 propionyl-CoA synthetase

Query= SwissProt::Q9H6R3
         (686 letters)



>NCBI__GCF_000733765.1:WP_043768476.1
          Length = 630

 Score =  683 bits (1762), Expect = 0.0
 Identities = 318/627 (50%), Positives = 442/627 (70%), Gaps = 3/627 (0%)

Query: 58  SGSEYKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPST-RWFVEGMLNICYNA 116
           +   Y+T +  S+ +PE FW + AE + W + W + L +  +    RWF  G LN CYNA
Sbjct: 2   AAGRYETEYRQSIDNPESFWAEQAEALHWERRWDRVLSHDDADGAPRWFAGGRLNTCYNA 61

Query: 117 VDRHIENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMP 176
           VDRH++ G+G++IA+I+DSPVT++   F++ E+ +  ++LAG L   G++ GD VVIYMP
Sbjct: 62  VDRHVDAGRGEQIALIHDSPVTDSVRRFSFIELRDATARLAGALRAAGVETGDRVVIYMP 121

Query: 177 MIPQAMYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVP 236
           MI +A   MLACARIGA+HS++FGGFA+ EL+ RID  KPK +++AS GIE  R + Y P
Sbjct: 122 MIAEAAIAMLACARIGAVHSVVFGGFAAPELAKRIDDAKPKAILSASCGIEGSRVIAYKP 181

Query: 237 LVEEALKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYI 296
           LV+ A++   HKP   LI  RP  EA  L+ GRD DW++ +A A   DCVPV +  PLY+
Sbjct: 182 LVDAAIEAASHKPQSCLILQRPQCEA-ELSAGRDRDWEQAVAAAGPADCVPVEATDPLYV 240

Query: 297 LYTSGTTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPL 356
           LYTSGTTG PKGV+R  GG+AV L +SM ++Y + PGEV+WAASD+GWVVGHSYI Y PL
Sbjct: 241 LYTSGTTGKPKGVVRDNGGHAVALTYSMKAVYDMNPGEVFWAASDVGWVVGHSYIVYAPL 300

Query: 357 LHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLT 416
           L G TTV++EGKPVGTPDAGA++RV +EHGV ALFTAPTA RAI+++DP      +Y L 
Sbjct: 301 LAGCTTVMFEGKPVGTPDAGAFWRVASEHGVKALFTAPTAFRAIKKEDPKGEHLARYKLA 360

Query: 417 RFKTLFVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAG 476
            F+ L++AGERCD +T++W+  + +VPV+DHWWQTETG P+ A C GL   + P  G AG
Sbjct: 361 AFEALYLAGERCDPDTIDWASGLLQVPVIDHWWQTETGWPVAAVCRGL-QDEAPHIGSAG 419

Query: 477 KSVPGYNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYD 536
           + VPGY++ +LDD+  ++    +GNIV++ PLPPG    LW N++ F+  Y  ++PG+Y 
Sbjct: 420 RPVPGYDIRVLDDDGHEVPRDAIGNIVIRQPLPPGTLPTLWNNEQGFRENYLARYPGHYL 479

Query: 537 TMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGH 596
           T DAG +D EGY++VMSR+DD+INVAGHR+S GA+EE +  H  VA+CAV+   D  KG 
Sbjct: 480 TGDAGKIDAEGYVWVMSRIDDIINVAGHRLSTGAMEEVLAGHPDVAECAVIAVADATKGQ 539

Query: 597 VPLALCVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALS 656
           +P+ + VL+  ++   E +  E+++ VR  IG VAAF+ A+ V +LPKTRSGK+ R  + 
Sbjct: 540 LPVGMVVLKSGVDRDTEVITRELIQRVRDEIGAVAAFKRAIVVPRLPKTRSGKVLRKTMR 599

Query: 657 AIVNGKPYKITSTIEDPSIFGHVEEML 683
           +I NG+   + +TI+DP+I   + E L
Sbjct: 600 SIANGENLTVPATIDDPAILDEIREAL 626


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: 1210
Number of extensions: 70
Number of successful extensions: 4
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: 630
Length adjustment: 38
Effective length of query: 648
Effective length of database: 592
Effective search space:   383616
Effective search space used:   383616
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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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