Alignments for a candidate for acs in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Sulfuritalea hydrogenivorans DSM 22779

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_041099580.1 SUTH_RS12165 propionate--CoA ligase

Query= curated2:O93730
         (670 letters)



>NCBI__GCF_000828635.1:WP_041099580.1
          Length = 630

 Score =  476 bits (1225), Expect = e-138
 Identities = 254/636 (39%), Positives = 389/636 (61%), Gaps = 21/636 (3%)

Query: 33  YFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRHV 92
           Y +F+++++E  + FW   +  ++W  P  K+ D S PPF  WFVGG+ NL + AVDRH 
Sbjct: 4   YAEFYKRSIEQRDDFWAEQSALIDWQTPPQKICDFSKPPFANWFVGGKTNLCHNAVDRHA 63

Query: 93  KTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITLY 152
                ++  +    E  +E  Y       T+ +L  EV R A ++K + GV +GD++ +Y
Sbjct: 64  AKRPNDRALVYISTETNEEKSY-------TFAELKSEVMRAAAIMK-SLGVGRGDRVLIY 115

Query: 153 LPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVRL 212
           +PM+ E    +LA  RIGAI SVVF GF++ +LA RI+D++ ++++++D   R GR V  
Sbjct: 116 MPMIAEATFAILACARIGAIHSVVFGGFASGSLATRIDDAKPKLIVSSDAGMRAGRAVPY 175

Query: 213 KEVVDAALEKAT-GVESVIVLPRLGLKDVPMTEGRDYWWNKLMQGIPPNAYIEPEPVESE 271
           K ++D A + A    E V+++ R   K  P   GRD  + +L +    NA +  E +ES 
Sbjct: 176 KHLLDEACKLAQFPPEKVLMIDRGLDKGWPKVAGRDVDYAEL-RAKHMNADVPCEWMEST 234

Query: 272 HPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSYV 331
            PS+ILYTSGTTGKPKG+  DTGG+AV + A+MK +F   + +  + T+DIGWV GHSY+
Sbjct: 235 EPSYILYTSGTTGKPKGVQRDTGGYAVALAASMKHIFQGGEGETMFSTSDIGWVVGHSYI 294

Query: 332 VLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKHD 391
           + GPL+ G   ++YEG P  P P  WW ++E+Y V + +++PTA+R+  +    W  K+D
Sbjct: 295 IYGPLIAGMATIMYEGTPIRPDPGIWWQLVEKYKVNVMFSAPTAVRVLKKSDNSWLHKYD 354

Query: 392 LSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVPMKP 451
           LS+L+ +   GEP++     W   ++G  K+     +W TETG  ++S   G+    +K 
Sbjct: 355 LSSLKHLFLAGEPLDQPTHEW---IMGELKLPVIDNYWQTETGWPILSTVRGVEDTKIKF 411

Query: 452 GTNGPPLPGFEVDVVDENGNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYWSRF- 509
           GT   P+ G+++ +  E+G       KG + I  P  PG L  IWGD +R++ TY+S F 
Sbjct: 412 GTPSFPVYGYDLRIFREDGTVCDANEKGIVGIVPPLPPGCLSTIWGDDDRFVSTYFSLFK 471

Query: 510 -PGMFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGVP 568
            P ++ + D+ IKD +GY ++LGR D+VI VAGHRLGT E+E A+  H AVAE AVVGV 
Sbjct: 472 EPQVYSSFDWGIKDDEGYHFILGRTDDVINVAGHRLGTREIEEAVQGHAAVAEVAVVGVS 531

Query: 569 DAIKGEVPIAFVVLKQGV-APSDELRKELREHVRRTI----GPIAEPAQIFFVTKLPKTR 623
           D +KG+ P+AF V+K      + ELR  L   +++ +    G IA P ++ FVT LPKTR
Sbjct: 532 DQLKGQEPVAFAVVKDPARIATPELRAALEAEIKKVVDGNLGAIARPKRVHFVTGLPKTR 591

Query: 624 SGKIMRRLLKAVATGAPLGDVTTLEDETSVEEAKRA 659
           SGK++RR ++A+A G   GD+TT++D +++E+ K A
Sbjct: 592 SGKMLRRSIQALAEGRDAGDLTTIDDPSTLEQIKAA 627


Lambda     K      H
   0.319    0.138    0.440 

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: 1161
Number of extensions: 68
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: 670
Length of database: 630
Length adjustment: 38
Effective length of query: 632
Effective length of database: 592
Effective search space:   374144
Effective search space used:   374144
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 Apr 09 2024. 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