Alignments for a candidate for acs in Porphyrobacter dokdonensis DSW-74

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Porphyrobacter dokdonensis DSW-74

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_086622008.1 I603_RS03965 AMP-binding protein

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_001677335.1:WP_086622008.1
          Length = 1808

 Score =  243 bits (621), Expect = 4e-68
 Identities = 174/517 (33%), Positives = 250/517 (48%), Gaps = 90/517 (17%)

Query: 220 VRNVIVYRRTGGK-VAWTEGRDRWMEDVSAGQ------------------------PD-- 252
           V  VIV R T    + W E RDRW  +++                           PD  
Sbjct: 316 VEAVIVCRHTNQPDMIWREERDRWSHELTDAALVTVLEKARDAGFAVHTADDLLALPDAD 375

Query: 253 -------TCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDD 305
                  + +  PV A++P+F +YTSGSTGKPKG+ HS G Y      TM  +FD +P D
Sbjct: 376 FVRAIWASSKPMPVDADYPMFFIYTSGSTGKPKGIVHSHG-YAAGVAETMAASFDARPGD 434

Query: 306 LFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPT 365
           + +  AD GW+TG +Y+   PL    T +V EG P +P+AGRF  MI RHKV+IF    T
Sbjct: 435 VLYVVADPGWITGQSYLICAPLMTRVTSLVSEGSPVFPHAGRFASMIERHKVAIFKAGVT 494

Query: 366 AIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQ 425
            ++S++  ++ D     ++YD+S LR+     EP++P    +  +++       ++++W 
Sbjct: 495 FLKSVM--SDPDNLADLQRYDMSGLRVATFCAEPVSPSVQAFGMEHVTPR---YINSYWA 549

Query: 426 TETGGHMITPLPGAT--PLVPGSCTLPLPGIMAAI----VDETGHDVP------------ 467
           TE GG   T + G    PL P +   PLP I+  +     D    DVP            
Sbjct: 550 TEHGGIAWTHMFGNDDFPLRPDAHAYPLPWIVGDVWVEDADGAPADVPFARSDAGGVPWR 609

Query: 468 ---NGNGGILVVKRPWPAMIRTIW------------------GDPERFRKSYFPEELGGK 506
               G  G +V+  P+P + RTIW                  GD  R+ + Y+    G  
Sbjct: 610 RAQTGEKGEIVIAAPYPYLARTIWGDIAGFKVEDGRVDPSWRGDAARWEEGYWKRWKGAW 669

Query: 507 LYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESALVSNPLVA------EAAV 560
            Y  GD +I+  D G F++ GR DDV+NVSGHRMGT EIE A++ +  +A         V
Sbjct: 670 AYTQGDFAIQHPD-GSFSLHGRSDDVINVSGHRMGTEEIEGAVLRDKALAPDSPVGNVLV 728

Query: 561 VGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAKPKDIRFGDNLPK 620
           VG P    G    AFVV    R   +  ++    L + V  E G +A P D       P+
Sbjct: 729 VGAPHREKGLTPLAFVVPVAGR---KLTIEDKRRLFDLVRAEKGAVAVPADFIEVSQFPE 785

Query: 621 TRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLK 657
           TRSGK MRR++R+L  GE++  D +TL NP  LE+L+
Sbjct: 786 TRSGKYMRRMVRALVVGEDV-GDVTTLRNPEALEELR 821



 Score = 98.2 bits (243), Expect = 3e-24
 Identities = 55/166 (33%), Positives = 90/166 (54%), Gaps = 13/166 (7%)

Query: 60  PFTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTR------ 113
           P+    D SN P ++WF  G  NA+++ LDR++  G+ D+ A++FE D   ++       
Sbjct: 64  PWHTGFDGSNPPHWRWFVGGRTNAAFSELDRHVLAGHGDEAALIFEGDRWDMSAMGGKGA 123

Query: 114 ------VTYRELHGKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSV 167
                 VT ++L  +V + A  L+ LG++ GDR+ + MP  V  +   +A  R+G  ++ 
Sbjct: 124 PIDCFTVTRKQLLLEVAKCAVALEQLGLKPGDRMALNMPSIVPQIYWTEAAKRMGVVYTA 183

Query: 168 VFGGFSAKSLQERLVDVGAVALITADEQMRGGKALPLK-AIADDAL 212
           VFGGFS K+L +R+ D  A  ++T+D   R  +    K A  D AL
Sbjct: 184 VFGGFSDKTLSDRIADTAARVIVTSDGSYRNAQVAAFKNAYTDPAL 229


Lambda     K      H
   0.319    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: 3071
Number of extensions: 189
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 660
Length of database: 1808
Length adjustment: 46
Effective length of query: 614
Effective length of database: 1762
Effective search space:  1081868
Effective search space used:  1081868
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 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:

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 2024 update 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