Alignments for a candidate for prpE in Thiohalospira halophila HL 3

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Thiohalospira halophila HL 3

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_093426890.1 BM272_RS00970 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_900112605.1:WP_093426890.1
          Length = 646

 Score =  851 bits (2198), Expect = 0.0
 Identities = 402/646 (62%), Positives = 502/646 (77%), Gaps = 4/646 (0%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQG-KILDWIKPYQKVKNTS 59
           MS+   + +P ++A R  +   +YEAMY++S++ P+ FW EQ  + LDW + +    + S
Sbjct: 1   MSEHKVYPVPESVAARAHVTQAEYEAMYRRSVDDPEGFWAEQADRFLDWFEKWDTTLDWS 60

Query: 60  FAPGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCR 119
           F  G+V ++W++ G LN+A NC+DRHL E+ ++TA+IWEGD+  Q +HI+++ELH  V R
Sbjct: 61  FE-GDVHVEWFKGGKLNVAHNCIDRHLAEHAEKTALIWEGDEPDQDQHITFRELHEQVSR 119

Query: 120 FANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSN 179
             N L E G+ KGD V +YMPM+PEA  AMLACARIGAVHSV+FGGFSPEA+  RI D+ 
Sbjct: 120 LGNVLKERGVSKGDRVCLYMPMIPEAVYAMLACARIGAVHSVVFGGFSPEALKDRIQDAE 179

Query: 180 SRLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHD 239
           + +VIT+DEGVR GR + LK N D A+      SV  V+ ++RTGG I W + RD+W+H+
Sbjct: 180 ASVVITADEGVRGGRKVGLKANTDKAVDQ--CPSVHTVLTVRRTGGDIGWNDSRDVWYHE 237

Query: 240 LVEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGD 299
            VE AS    AE M+AEDPLFILYTSGSTGKPKGVLHTTGGYL+YAA+T  Y FD  P D
Sbjct: 238 AVEAASADCPAEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLYAAITTWYTFDLQPDD 297

Query: 300 IYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPT 359
           +YWCTADVGW+TGHSYL+YGPLA   T+++FEGVP++P  +R  +VVDKHQV++ YTAPT
Sbjct: 298 VYWCTADVGWITGHSYLVYGPLANATTSVVFEGVPSYPDASRFWEVVDKHQVSVFYTAPT 357

Query: 360 AIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETG 419
           AIRALM EGD+ +  TDRSSLRILG+VGEPINPEAWEWY+  +G E+CP+VDTWWQTETG
Sbjct: 358 AIRALMREGDEPVTKTDRSSLRILGTVGEPINPEAWEWYYHVVGKEQCPIVDTWWQTETG 417

Query: 420 GFMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFG 479
           G +ITPLPGATELK GSATRPFFG+ PAL+D +G+ +EG  EG+LVIT  WPGQ RT++G
Sbjct: 418 GHLITPLPGATELKPGSATRPFFGIVPALMDTDGHVVEGEGEGALVITRPWPGQMRTIYG 477

Query: 480 DHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAH 539
           +H+RF +TYFS FK  YFSGDGARRD +G YWITGR+DDVLNVSGHR+GTAEIESALV H
Sbjct: 478 NHQRFVETYFSAFKGCYFSGDGARRDGNGDYWITGRMDDVLNVSGHRMGTAEIESALVLH 537

Query: 540 PKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWT 599
             +AEAAVVG PH++KGQ IYAYV L    EPS  L  E+ N VR EIGP+A+PD + W 
Sbjct: 538 DAVAEAAVVGYPHDVKGQGIYAYVILVKDAEPSDALRKELVNLVRSEIGPIASPDAIQWA 597

Query: 600 DSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
             LPKTRSGKIMRRILRKIAA +  +LGDTSTLADP VV++L+  +
Sbjct: 598 PGLPKTRSGKIMRRILRKIAANELDSLGDTSTLADPAVVDELINNR 643


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: 1512
Number of extensions: 69
Number of successful extensions: 3
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: 652
Length of database: 646
Length adjustment: 38
Effective length of query: 614
Effective length of database: 608
Effective search space:   373312
Effective search space used:   373312
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: 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