Alignments for a candidate for prpE in Brucella microti CCM 4915

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Brucella microti CCM 4915

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_002964888.1 BMI_RS08370 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000022745.1:WP_002964888.1
          Length = 651

 Score =  884 bits (2283), Expect = 0.0
 Identities = 419/633 (66%), Positives = 502/633 (79%), Gaps = 5/633 (0%)

Query: 18  LINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNL 77
           LI+ + Y   Y++S++ PD FW + G+ +DW KP+ KVKNT F  G+V+IKWYEDG  N+
Sbjct: 17  LIDNETYLEWYEESVSDPDGFWAKHGRRIDWFKPFTKVKNTDFN-GDVTIKWYEDGVTNV 75

Query: 78  AANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAI 137
           + NC+DRHL+  GD+ AIIWEGD+    K I+Y+EL+ +VCR AN L + G+KKGD V I
Sbjct: 76  SYNCIDRHLKSRGDKVAIIWEGDNPYIDKKITYRELYENVCRMANVLKKHGVKKGDRVTI 135

Query: 138 YMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIP 197
           Y+PM+PEAA AMLACARIGAVHSV+F GFSPEA+AGRI+D  S  VIT+DEGVR G+ + 
Sbjct: 136 YLPMIPEAAYAMLACARIGAVHSVVFAGFSPEALAGRIVDCESTFVITADEGVRGGKPVA 195

Query: 198 LKKNVDDALK--NPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNA 255
           LK+N D A+         V  V+V++RTGGK+ W  GRDLW+H  V       + E MNA
Sbjct: 196 LKENTDTAIDIAAKQYVMVNKVLVVRRTGGKVSWGRGRDLWYHQEVASVEPHCEPEPMNA 255

Query: 256 EDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSY 315
           EDPLFILYTSGSTGKPKGVLHTTGGYLVYA++T +YVFDYH G+IYWCTADVGWVTGHSY
Sbjct: 256 EDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYHDGEIYWCTADVGWVTGHSY 315

Query: 316 LLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGT 375
           ++YGPLA GATTLMFEGVPN+P   R  +VVDKH VNI YTAPTA+RALM  GD+ +  +
Sbjct: 316 IVYGPLANGATTLMFEGVPNFPDQGRFWEVVDKHHVNIFYTAPTALRALMGAGDEFVTRS 375

Query: 376 DRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAG 435
            RS+LR+LGSVGEPINPEAWEWY+  +G++KCP+VDTWWQTE GG +ITPLPGAT+LK G
Sbjct: 376 SRSTLRLLGSVGEPINPEAWEWYYNVVGDQKCPIVDTWWQTENGGILITPLPGATDLKPG 435

Query: 436 SATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNM 495
           SATRPFFGV+P LVDNEGN  EG  +G+L I+DSWPGQ RT++GDH+RF +TYFST+K M
Sbjct: 436 SATRPFFGVKPVLVDNEGNVQEGVADGNLCISDSWPGQMRTVYGDHKRFIETYFSTYKGM 495

Query: 496 YFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIK 555
           YFSGDG RRDEDGYYWITGRVDDVLN+SGHRLGTAEIESALV+H  ++EAAVVG PH IK
Sbjct: 496 YFSGDGCRRDEDGYYWITGRVDDVLNISGHRLGTAEIESALVSHHSVSEAAVVGYPHPIK 555

Query: 556 GQAIYAYVTLNHGEEPS--PELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRR 613
           GQ IY YVTL  G +     EL  E+   VRKEIGP+ATPD + +   LPKTRSGKIMRR
Sbjct: 556 GQGIYCYVTLMTGADAQDPDELRKELVQHVRKEIGPIATPDKIQFAPGLPKTRSGKIMRR 615

Query: 614 ILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
           ILRKIA  +   LGDTSTLADPGVV+ L+E +Q
Sbjct: 616 ILRKIAEDEFGALGDTSTLADPGVVDDLIENRQ 648


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: 1501
Number of extensions: 55
Number of successful extensions: 4
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: 651
Length adjustment: 38
Effective length of query: 614
Effective length of database: 613
Effective search space:   376382
Effective search space used:   376382
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 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