Alignments for a candidate for acs in Brucella microti CCM 4915

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Brucella microti CCM 4915

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_002968065.1 BMI_RS00095 acetoacetate--CoA ligase

Query= curated2:Q9X928
         (651 letters)



>NCBI__GCF_000022745.1:WP_002968065.1
          Length = 662

 Score =  229 bits (585), Expect = 2e-64
 Identities = 187/614 (30%), Positives = 284/614 (46%), Gaps = 33/614 (5%)

Query: 39  DRLGFWAEQARRLTW-------AKEPTETLDWSNPPFAKWFKDGTLNVAYNCVDRHVEAG 91
           DR GFW     +L W        +  T   D  +   AK+F +  LN A N + RH    
Sbjct: 57  DRAGFW-----QLVWDFCAVIGERGNTALTDRGHMRAAKFFPEARLNFAENLL-RH---- 106

Query: 92  NGDRVAIHFEGESGDSRALTYAQLKDEVSKAANALLELGVQKGDRVAIYMPMIPETAIAM 151
            GD  AI F GE+   R LT+  L   VSK    +L  GVQ GDRVA  MP +PE    M
Sbjct: 107 KGDGEAIVFRGENKVERRLTWNDLHALVSKLQQFMLSEGVQPGDRVAGMMPNMPEAVALM 166

Query: 152 LACARIGAAHSVVFGGFSSDALATRIQDADARVVITADGGYRRGKPSALKPAVDEAVERA 211
           LA + IGA  S     F    +  R    + ++    DG +  GK  A+   V E   + 
Sbjct: 167 LAASSIGAVWSSCSPDFGVQGVLDRFGQIEPKLFFACDGYWYNGKRIAVADKVAEVTAKL 226

Query: 212 GIVEHVLVVRRTGQDVAWDDSRDKWWH-----ETVDGQSAEHTPEAFDAEHPLFILYTSG 266
             ++  ++V   G+  A  D  +K        E    +  E T   FD  HPL+IL++SG
Sbjct: 227 PGLKRAVIVTYLGEAEAVADKAEKGIALYAALEPFKAKPVEFTQLPFD--HPLYILFSSG 284

Query: 267 TTGKPKGILHTSGGYLTQTAYTHWAVFDLKPETDVFWCTADVGWVTGHSYIVYGPLANGA 326
           TTG PK I+H +GG L Q    H    DL+ + D F+     GW+   +++  G +A+GA
Sbjct: 285 TTGIPKCIVHRAGGVLLQHLKEHRLHADLR-DGDRFFYFTTCGWMM-WNWLASG-IASGA 341

Query: 327 TQVMYEGTPDTPHQGRFWEIVQKYGVTILYTAPTAIRTFMKWGDDIPAKFDLSSLRVLGS 386
           T ++Y+G+P  P     ++     G+T   T+   I   +K G       DLS+LR + S
Sbjct: 342 TLMLYDGSPFYPDGNVLFDYAAAEGMTYFGTSAKFIDAVLKAGLKPGETHDLSALRTISS 401

Query: 387 VGEPINPEAWIWYRKNIGADATPVVDTWWQTETGAMMITPLPGVTHAKPGSAQRPLPGIS 446
            G P++PE + +    I  D   +      T+  +  +  +P       G  Q    G++
Sbjct: 402 TGSPLSPEGFAFVYDAIKKD-VHLASISGGTDIVSCFVLGVP-TEPVWQGEIQGAGLGMA 459

Query: 447 ATVVDDEANEVPNGGGGYLVLTEPWPSMLRTIWGDDQ--RFIDTYWSRFEGKYFAGDGAK 504
             V +D+   V  G  G LV T+ +PSM    W D Q  ++   Y+ RF+  +  GD A+
Sbjct: 460 VDVWNDDGKPV-RGEKGELVCTKAFPSMPLQFWNDAQGEKYQAAYFERFDNIWCHGDFAE 518

Query: 505 KDDDGDIWLLGRVDDVMLVSGHNISTTEVESALVSHPSVAEAAVVGATDETTGQAIVAFV 564
             + G I + GR D  +   G  I T E+ + +   P +AEA  +G  D      +V FV
Sbjct: 519 WTEHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQMPEIAEALCIG-QDWDRDVRVVLFV 577

Query: 565 ILRGTTAESEDLVAELRNHVGATLGPIAKPKRILPVSELPKTRSGKIMRRLLRDVAENRQ 624
            L       +DL A +R  +     P   P +I+ V ++P+T+SGKI+   +RD+   R+
Sbjct: 578 RLAEGVVLDDDLKARIRTKIRTGATPRHVPAKIIAVRDIPRTKSGKIVELAVRDIVHGRE 637

Query: 625 VGDVTTLADSTVMD 638
           V +   LA+   ++
Sbjct: 638 VKNREALANPEALE 651


Lambda     K      H
   0.316    0.133    0.410 

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: 1101
Number of extensions: 73
Number of successful extensions: 5
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: 651
Length of database: 662
Length adjustment: 38
Effective length of query: 613
Effective length of database: 624
Effective search space:   382512
Effective search space used:   382512
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 (21.6 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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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