Alignments for a candidate for acs in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Sinorhizobium meliloti 1021

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate SMc00774 SMc00774 acetoacetyl-CoA synthetase

Query= SwissProt::A0R5G1
         (940 letters)



>FitnessBrowser__Smeli:SMc00774
          Length = 650

 Score =  185 bits (469), Expect = 9e-51
 Identities = 177/601 (29%), Positives = 270/601 (44%), Gaps = 61/601 (10%)

Query: 355 AKWFVGGKINVAYNCVDRHVEAGNGDRVAIHWEGEPVGDARSITYAELKDEVCKAANALT 414
           A++F   ++N A N + +    G+GD  A+ + GE     R +T+ EL+  V +   AL 
Sbjct: 80  ARFFPEARLNFAENLLRK---TGSGD--ALIFRGEDKVSYR-LTWDELRALVSRLQQALR 133

Query: 415 DLGLVAGDRVAIYMPMIPEAIVAMLACARLGVMHSVVFAGFSASALRARIEDAEAKLVIT 474
             G+ AGDRVA  MP +PE I  MLA A +G + S     F    +  R      KL I 
Sbjct: 134 AQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQIAPKLFIV 193

Query: 475 SDGQYRRGKAASLKEAVDEAVADQPSVKNVLVVRRTGIDVKWTDGRDLWWDETVEQAST- 533
            DG +  GK   +   V  AVA       V+V            G       TVE   T 
Sbjct: 194 CDGYWYNGKRQDVDSKV-RAVAKSLGAPTVIVPYA---------GDSAALAPTVEGGVTL 243

Query: 534 -------EHIPAAFDS---EQPLFLLYTSGTTGKPKGIVHTSGGYLTQSSYTHWNVFDVK 583
                  +  P  F+      PL++L++SGTTG PK IVH++GG L Q    H     ++
Sbjct: 244 ADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGLR 303

Query: 584 PESDVYWCTADIGWVTGHTYIVYGPLSNGVTQVVYEGTPTSPTEHRHFEVIEKYGVTIYY 643
               +++ T   GW+  + ++  G L+ G T  +Y+G+P  P  +  F+        ++ 
Sbjct: 304 DGERLFYFTT-CGWMMWN-WLASG-LAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFG 360

Query: 644 TAPTLIRTFMKLGHQIPASHDLSSLRLLGSVGEPINPEAWRWYREHIG--------GGKT 695
           T+   I    K G     +HDLSSLRL+ S G P++PE + +  E I          G T
Sbjct: 361 TSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGT 420

Query: 696 PIVDTWWQTETGAIMISPLPGVTAAKPGSAMTPLPGISAKIVDDEGNQLVPGADEAEHVT 755
            IV  +       ++ +PL  V     G    P  G++  + +DEG  +           
Sbjct: 421 DIVSCF-------VLGNPLKPVWR---GEIQGPGLGLAVDVWNDEGKPV-------RGEK 463

Query: 756 GYLVLDQPWPAMLRGIWGDPQ--RFKDTYWSRFAEQGWYFAGDGARYDSDGHIWVLGRID 813
           G LV  + +P+M    W DP   +++  Y+ RF +  W   GD A +   G I + GR D
Sbjct: 464 GELVCTRAFPSMPVMFWNDPDGAKYRAAYFDRF-DNVWCH-GDFAEWTPHGGIVIHGRSD 521

Query: 814 DVMNVSGHRISTAEVESALVGHAGVAEAAVVGASDDTTGQAICAFVILKASAHGGPENMI 873
             +N  G RI TAE+ + +     VAEA  +G  D      +  FV L A      E + 
Sbjct: 522 ATLNPGGVRIGTAEIYNQVEQMDEVAEALCIG-QDWEDDVRVVLFVRL-ARGVELTEALT 579

Query: 874 EELRAEVAREISPIAKPREIHIVPELPKTRSGKIMRRLLRDVAEGRELGDTSTLVDPSVF 933
            E++  +    SP   P +I  V ++P+T+SGKI+   +RDV  GR + +   L +P   
Sbjct: 580 REIKNRIRSGASPRHVPAKIIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEAL 639

Query: 934 E 934
           +
Sbjct: 640 D 640


Lambda     K      H
   0.315    0.129    0.395 

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: 1468
Number of extensions: 61
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 940
Length of database: 650
Length adjustment: 41
Effective length of query: 899
Effective length of database: 609
Effective search space:   547491
Effective search space used:   547491
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: 55 (25.8 bits)

This GapMind analysis is from Sep 17 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 paper from 2022 on GapMind for carbon sources, or view the source code.

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