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:

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:

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:

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:

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