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

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE 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::P31638
         (660 letters)



>NCBI__GCF_001580365.1:WP_062735310.1
          Length = 708

 Score =  518 bits (1335), Expect = e-151
 Identities = 289/650 (44%), Positives = 392/650 (60%), Gaps = 70/650 (10%)

Query: 69  NAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFAN 128
           + P   WFE G LN ++NC+DR+++ G    VA+ FE + G     TY +L  +V R AN
Sbjct: 63  SVPELAWFEGGRLNVAHNCVDRHVEAGRGAHVALYFEGEPGDRLVYTYADLQREVSRAAN 122

Query: 129 GLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVA 188
            L ALG+ +GDRVVIY+P+  E VV   ACAR+GA HS+VFGGFSA++L+ R+ D GA  
Sbjct: 123 ALLALGVERGDRVVIYLPVIPETVVITLACARIGAVHSLVFGGFSAEALRFRVEDTGAKV 182

Query: 189 LITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTG------------------ 230
           L+T D Q R G  +P+KA+AD+A +  G  A+ +V+V RRT                   
Sbjct: 183 LVTTDGQHRRGAVVPVKAVADEACS--GDNAIEHVVVVRRTSRPGRSDLPRGTRGTHSKE 240

Query: 231 -GKVAWTEGRDRWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLL 289
              V WT GRD W  ++ A QPD  EAE   AE PLF++YTSG+TG+PKG+ H+ GGYL+
Sbjct: 241 EDAVPWTRGRDVWWHELVAEQPDVHEAEAFDAESPLFIIYTSGTTGRPKGLVHTMGGYLV 300

Query: 290 WALMTMKWTFDIKPD------------------------DLFWCTADIGWVTGHTYIAYG 325
            A  T    FD+ PD                         + WCTAD+ WVT HTY  YG
Sbjct: 301 QAAYTHALLFDLLPDVRDDEGRLRPDELSTVNDPAKVDSTVHWCTADLAWVTAHTYEIYG 360

Query: 326 PLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLIKAAEADEKIHPKQY 385
           PL  G ++V++EG P  P+ GR +++I R+ V+ +YTAPT IRSL+ A     K  P  Y
Sbjct: 361 PLVNGVSEVIYEGTPNTPHWGRHFEVIERYGVTTYYTAPTLIRSLMGAF---PKGVPPLY 417

Query: 386 DLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTETGGHMITPLP-------- 437
           +L+S+RLLG+VGE +NPEAW W    +G +  P VDT+WQ+ETG  +++P P        
Sbjct: 418 NLNSVRLLGSVGESVNPEAWRWLRAQLGRDEVPFVDTWWQSETGATVMSPRPHDPQFAPP 477

Query: 438 -----GA--TPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIWGD 490
                GA  T L PG  T  +PG+   +VDE G  VP G  G +VV R  P+M RT+WGD
Sbjct: 478 GTFDDGAPHTALKPGCATRAVPGLSTRVVDEAGATVPPGVQGFVVVDRTGPSMARTVWGD 537

Query: 491 PERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESALV 550
           P+R+  SY+        +LAGDG+  D++ G   I+GR+DDV+NVSGHR+ T+EIESALV
Sbjct: 538 PQRYLSSYWQAYAEQGWFLAGDGARCDEE-GDIYILGRVDDVINVSGHRLSTIEIESALV 596

Query: 551 SNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEE--AVKIATELRNWVGKEIGPIAK 608
           ++P V EA      D++TG A+ A+VVL    P  E   A ++   LR  V +EIGPIAK
Sbjct: 597 THPWVVEAGAAPVRDELTGHAVLAYVVL---TPEAERVPADELTATLREHVAREIGPIAK 653

Query: 609 PKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658
           P+ +    +LPKTRSGKI RRLL  L +GE +  D S+L+N   LE++ +
Sbjct: 654 PRAVVAVPDLPKTRSGKITRRLLAQLWEGEPL-GDRSSLQNEEALERIAE 702


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: 1423
Number of extensions: 67
Number of successful extensions: 7
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: 660
Length of database: 708
Length adjustment: 39
Effective length of query: 621
Effective length of database: 669
Effective search space:   415449
Effective search space used:   415449
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: 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