Alignments for a candidate for prpE in Pontibacillus litoralis JSM 072002

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Pontibacillus litoralis JSM 072002

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_036835183.1 N784_RS11885 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000775615.1:WP_036835183.1
          Length = 571

 Score =  383 bits (984), Expect = e-110
 Identities = 222/571 (38%), Positives = 327/571 (57%), Gaps = 34/571 (5%)

Query: 66  SIKWYEDGTLNLAANCLDRHLQE--NGDRTAIIWEGDDASQSKHISYKELHRDVCRFANT 123
           +  W   G +N+A   +DRH +     D+ A+I+   D  ++   ++ +L +   +FAN 
Sbjct: 33  AFSWSRTGKVNIAYEAIDRHAENPMKTDQVALIYSSPDREET--YTFSDLKQSSNQFANV 90

Query: 124 LLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLV 183
           L + GI+KGD V I+MP  PE   A     ++GA+   +F  F  +AV  R+ DS + ++
Sbjct: 91  LKKYGIEKGDRVFIFMPRSPEFYSAFFGILKVGAIAGPLFEAFMEQAVRDRLEDSEASML 150

Query: 184 ITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQ 243
           +T+ E +     +P K+          +  ++ +V++    G+ D +EG  + +H+ + Q
Sbjct: 151 VTTPELLER---VPHKE----------LAHLKQIVLV----GEDDNKEGSFIDFHEEMNQ 193

Query: 244 ASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWC 303
           AS     E ++ ED + + YTSGSTGKPKGV H     + +   T K+V D H  D+YWC
Sbjct: 194 ASKSFDVEWVDLEDGMLLHYTSGSTGKPKGVYHVHHAMIQHYQ-TAKWVLDLHENDVYWC 252

Query: 304 TADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRA 363
           TAD GWVTG SY ++GP   G T ++  G  +   P    + +  ++V + Y+APTA R 
Sbjct: 253 TADPGWVTGTSYGIFGPWLNGVTNVVVGGRFS---PENWYKTLQDYEVTVWYSAPTAFRK 309

Query: 364 LMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMI 423
           LM+ G +AIE  D S LR + SVGEP+NPE   W  +     K  + DTWW TETG  +I
Sbjct: 310 LMSAGSQAIEPFDLSKLRHITSVGEPLNPEVIVWGLEAF---KLRIHDTWWMTETGAQVI 366

Query: 424 TPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHER 483
              P A ++K GS  +P  GV  +++DNEGN L     G+L I   WP   R ++   E+
Sbjct: 367 CNYP-AIDIKPGSMGKPVPGVVASIIDNEGNELPPNQMGNLAIKAPWPSMMRAIWKRPEK 425

Query: 484 FEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIA 543
           +E +YF    N Y SGD A  DE+GY+W  GR+DDV+N SG R+G  E+ES L+ HP +A
Sbjct: 426 YE-SYF--LNNWYISGDSAYYDEEGYFWFQGRLDDVINTSGERVGPFEVESKLIEHPAVA 482

Query: 544 EAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLP 603
           EA V+G PH  +G+ I A++TLN G   S EL  ++R +V+K +   ATP  L   DS+P
Sbjct: 483 EAGVIGKPHPERGEIIKAFITLNEGYVQSDELLDDIRQFVKKGLSAHATPRELEVKDSIP 542

Query: 604 KTRSGKIMRRILRKIAAGDTSNLGDTSTLAD 634
           KTRSGKIMRR+L+    G  +  GD STL +
Sbjct: 543 KTRSGKIMRRLLKSWELGLPT--GDVSTLEE 571


Lambda     K      H
   0.317    0.135    0.421 

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: 1114
Number of extensions: 73
Number of successful extensions: 9
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: 652
Length of database: 571
Length adjustment: 37
Effective length of query: 615
Effective length of database: 534
Effective search space:   328410
Effective search space used:   328410
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: 53 (25.0 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