Alignments for a candidate for acs in Kocuria turfanensis HO-9042

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Kocuria turfanensis HO-9042

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_062735310.1 AYX06_RS07950 AMP-binding protein

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_001580365.1:WP_062735310.1
          Length = 708

 Score =  652 bits (1681), Expect = 0.0
 Identities = 341/687 (49%), Positives = 432/687 (62%), Gaps = 84/687 (12%)

Query: 36  RLAFWAKQANRLSWTTPFTEVLDWSG---------------APFAKWFVGGELNVAYNCV 80
           R+AFW  QA+RL W  P+T    + G                P   WF GG LNVA+NCV
Sbjct: 23  RVAFWEGQASRLDWAGPWTTAHRFEGPRRIGQDADGNPTWSVPELAWFEGGRLNVAHNCV 82

Query: 81  DRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKAANALTDLGLVAGDRVAIYLPL 140
           DRHVEAG G  VA+++EGEP GDR   TY+DL  EVS+AANAL  LG+  GDRV IYLP+
Sbjct: 83  DRHVEAGRGAHVALYFEGEP-GDRLVYTYADLQREVSRAANALLALGVERGDRVVIYLPV 141

Query: 141 IPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQAKLLITADGQFRRGKPSPLKAA 200
           IPE V+  LACAR+G +HS+VFGGF+A AL+ R+ D  AK+L+T DGQ RRG   P+KA 
Sbjct: 142 IPETVVITLACARIGAVHSLVFGGFSAEALRFRVEDTGAKVLVTTDGQHRRGAVVPVKAV 201

Query: 201 ADEALAAIPDCSVEHVLVVRRTGIE-------------------MAWSEGRDLWWHHVVG 241
           ADEA +   D ++EHV+VVRRT                      + W+ GRD+WWH +V 
Sbjct: 202 ADEACSG--DNAIEHVVVVRRTSRPGRSDLPRGTRGTHSKEEDAVPWTRGRDVWWHELVA 259

Query: 242 SASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDVKPD---- 297
                H  E FD+E PLF++YTSGTTG+PKG++HT GGYL Q  YT   +FD+ PD    
Sbjct: 260 EQPDVHEAEAFDAESPLFIIYTSGTTGRPKGLVHTMGGYLVQAAYTHALLFDLLPDVRDD 319

Query: 298 -------------------SDVFWCTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPD 338
                              S V WCTAD+ WVT HTY +YGPL NGV+EV+YEGTP+TP 
Sbjct: 320 EGRLRPDELSTVNDPAKVDSTVHWCTADLAWVTAHTYEIYGPLVNGVSEVIYEGTPNTPH 379

Query: 339 RHRHFQIIEKYGVTIYYTAPTLIRMFM-KWGREIPDSHDLSSLRLLGSVGEPINPEAWRW 397
             RHF++IE+YGVT YYTAPTLIR  M  + + +P  ++L+S+RLLGSVGE +NPEAWRW
Sbjct: 380 WGRHFEVIERYGVTTYYTAPTLIRSLMGAFPKGVPPLYNLNSVRLLGSVGESVNPEAWRW 439

Query: 398 YRDVIGGGRTPLVDTWWQTETGSAMISPLPGI---------------AAAKPGSAMTPLP 442
            R  +G    P VDTWWQ+ETG+ ++SP P                  A KPG A   +P
Sbjct: 440 LRAQLGRDEVPFVDTWWQSETGATVMSPRPHDPQFAPPGTFDDGAPHTALKPGCATRAVP 499

Query: 443 GISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQPWPSMLRGIWGDPARYWHSYWSKFSDKG 502
           G+S ++VD+ G  +PP       V G++V+D+  PSM R +WGDP RY  SYW  ++++G
Sbjct: 500 GLSTRVVDEAGATVPPG------VQGFVVVDRTGPSMARTVWGDPQRYLSSYWQAYAEQG 553

Query: 503 YYFAGDGARIDPDGAIWVLGRIDDVMNVSGHRISTAEVESALVAHSGVAEAAVVGVTDET 562
           ++ AGDGAR D +G I++LGR+DDV+NVSGHR+ST E+ESALV H  V EA    V DE 
Sbjct: 554 WFLAGDGARCDEEGDIYILGRVDDVINVSGHRLSTIEIESALVTHPWVVEAGAAPVRDEL 613

Query: 563 TTQAICAFVVL--RANYAPHDRTAEELRTEVARVISPIARPRDVHVVPELPKTRSGKIMR 620
           T  A+ A+VVL   A   P D     LR  VAR I PIA+PR V  VP+LPKTRSGKI R
Sbjct: 614 TGHAVLAYVVLTPEAERVPADELTATLREHVAREIGPIAKPRAVVAVPDLPKTRSGKITR 673

Query: 621 RLLRDVAENRELGDTSTLLDPTVFDAI 647
           RLL  + E   LGD S+L +    + I
Sbjct: 674 RLLAQLWEGEPLGDRSSLQNEEALERI 700



 Score = 28.9 bits (63), Expect = 8e-04
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 96  WEGEPVGDRRTLTYSDLLAEVSKAANA 122
           WEGEP+GDR +L   + L  +++   A
Sbjct: 680 WEGEPLGDRSSLQNEEALERIAEVLAA 706


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: 1581
Number of extensions: 98
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: 2
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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Protein sequences (fasta format)
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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