Alignments for a candidate for acs in Kocuria flava HO-9041

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Kocuria flava HO-9041

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_058857233.1 AS188_RS00755 AMP-binding protein

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_001482365.1:WP_058857233.1
          Length = 708

 Score =  651 bits (1680), Expect = 0.0
 Identities = 343/692 (49%), Positives = 439/692 (63%), Gaps = 86/692 (12%)

Query: 32  AEEDRLAFWAKQANRLSWTTPFTEVL----------------DWSGAPFAKWFVGGELNV 75
           ++E R+AFW  QA+RL W  P+                     WS  P   WF GG+LNV
Sbjct: 19  SDEARVAFWETQASRLDWAEPWRTAHRFERPRRIGEDEDGSPTWS-VPEIAWFEGGKLNV 77

Query: 76  AYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKAANALTDLGLVAGDRVA 135
           A+NCVDRHVEAG G  VA+++EGEP GDR   TY+DL  EV++AA+ALT LG+  GDRV 
Sbjct: 78  AHNCVDRHVEAGRGAHVALYFEGEP-GDRLVYTYADLQREVARAAHALTALGVEQGDRVV 136

Query: 136 IYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQAKLLITADGQFRRGKPS 195
           IYLP+IPE VI  LACAR+G +HS+VFGGF+A AL+ R+ D  AK+L+T DGQ RRG   
Sbjct: 137 IYLPVIPETVIITLACARIGAVHSLVFGGFSAEALRFRVEDTGAKVLVTTDGQHRRGAVV 196

Query: 196 PLKAAADEALAAIPDCSVEHVLVVRRT-------------GIE------MAWSEGRDLWW 236
           P+KA ADEA +   + ++EHV+VVRRT             G+       + W+ GRD+WW
Sbjct: 197 PVKAVADEACSG--ENAIEHVVVVRRTSRPGRADLPRGTRGVRSKEEDAVPWTPGRDVWW 254

Query: 237 HHVVGSASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDVKP 296
           H ++      H  + FD+E PLF++YTSGTTGKPKG++HT GGYL Q  YT   +FD+ P
Sbjct: 255 HQLIADRPEVHEAQAFDAETPLFIIYTSGTTGKPKGLVHTMGGYLVQAAYTHALLFDLLP 314

Query: 297 DSD-----------------------VFWCTADIGWVTGHTYGVYGPLCNGVTEVLYEGT 333
           D +                       V WCTAD+ WVT HTY +YGPL NGVTEV+YEGT
Sbjct: 315 DVEDEDGVPRPDELSAVNDPAKVDATVHWCTADLAWVTAHTYEIYGPLVNGVTEVIYEGT 374

Query: 334 PDTPDRHRHFQIIEKYGVTIYYTAPTLIRMFM-KWGREIPDSHDLSSLRLLGSVGEPINP 392
           P+TP   RHF++IE+YGVT YYTAPTLIR  M  + + +P  ++L+S+RLLGSVGE INP
Sbjct: 375 PNTPHWGRHFEVIERYGVTAYYTAPTLIRSLMGAFPKGVPPLYNLNSIRLLGSVGESINP 434

Query: 393 EAWRWYRDVIGGGRTPLVDTWWQTETGSAMISPLPGI---------------AAAKPGSA 437
           EAWRW R  +G    P VDTWWQ+ETG+ ++SP P                  A KPG A
Sbjct: 435 EAWRWLRAQVGRDEVPFVDTWWQSETGATVMSPRPHDPQFAPPGTFPPGTPRTAPKPGCA 494

Query: 438 MTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQPWPSMLRGIWGDPARYWHSYWSK 497
              +PGIS ++VD+ G P+PP       V G++V+D   PSM R +WGDP RY  SYW  
Sbjct: 495 TRAVPGISTRVVDEDGAPVPPG------VQGFVVVDAIGPSMARTVWGDPQRYLSSYWQA 548

Query: 498 FSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHRISTAEVESALVAHSGVAEAAVVG 557
           ++++G++ AGDGAR D +G I++LGR+DDV+NVSGHR+ST E+ESALV H  V EA    
Sbjct: 549 YAEQGWFLAGDGARCDEEGDIYILGRVDDVINVSGHRLSTIEIESALVTHPWVVEAGAAP 608

Query: 558 VTDETTTQAICAFVV--LRANYAPHDRTAEELRTEVARVISPIARPRDVHVVPELPKTRS 615
           V DE T  A+ AFVV       AP +     LR  VAR I PIA+PR V  VP+LPKTRS
Sbjct: 609 VRDELTGHAVLAFVVPTREGAQAPAEELTRVLREHVAREIGPIAKPRAVVAVPDLPKTRS 668

Query: 616 GKIMRRLLRDVAENRELGDTSTLLDPTVFDAI 647
           GKI RRLL  + + +ELGD S+L +    + I
Sbjct: 669 GKITRRLLAQLWDGQELGDRSSLQNEEALEHI 700


Lambda     K      H
   0.319    0.136    0.433 

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: 1626
Number of extensions: 95
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 651
Length of database: 708
Length adjustment: 39
Effective length of query: 612
Effective length of database: 669
Effective search space:   409428
Effective search space used:   409428
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 (21.8 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)
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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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