Aligments for a candidate for acs in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Cupriavidus basilensis 4G11

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate RR42_RS10650 RR42_RS10650 acetyl-CoA synthetase

Query= SwissProt::P39062
         (572 letters)



>FitnessBrowser__Cup4G11:RR42_RS10650
          Length = 588

 Score =  519 bits (1337), Expect = e-151
 Identities = 272/571 (47%), Positives = 355/571 (62%), Gaps = 17/571 (2%)

Query: 14  NLKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEK 73
           NL +YE   R F WA   +  +    G LN A++A+DRHA S  + K A           
Sbjct: 19  NLGDYEAERRVFSWAAVSRELADQPQGALNIAWQAVDRHAASSLRGKAAFRILARGTPTH 78

Query: 74  Y-TFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEA 132
           + T+ ++   +NR  NVLR  G V KG+R+FI   R PELY  +LG++K G    PLF A
Sbjct: 79  FVTYGQLSALTNRFCNVLRDLG-VGKGERLFILAGRIPELYIAILGSLKNGTAVSPLFSA 137

Query: 133 FMEGAVKDRLENSEAKVVVTTPELLERIPV---DKLPHLQHVFVV----GGEAESGTNII 185
           F    +  R+   E  V+VTT  L ER      D++P L+HV +V    G  A  GT  +
Sbjct: 138 FGPDPIATRVNLGEGAVLVTTDMLFERKIAKWRDRMPSLKHVLLVAEDGGTTAVPGT--L 195

Query: 186 NYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLK 245
           +        S   +I     +D  LLH+TSG+TGTPKG +HVH A++  + TG++ LDL 
Sbjct: 196 DLSSLMASASDACEITPTTAEDMALLHFTSGTTGTPKGAVHVHGAVLTHWSTGRYALDLH 255

Query: 246 EEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPT 305
            +DIYWCTADPGWVTGT YG+ AP L+G T+++    F  E WY  ++  GV++WY+APT
Sbjct: 256 VDDIYWCTADPGWVTGTSYGVIAPLLHGVTSIVDREEFDAERWYAILQDEGVSIWYTAPT 315

Query: 306 AFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQL 365
           A RMLM AG ++A KY    LR   SVGEPLNPE + WG +V     HD WW TETG  +
Sbjct: 316 AIRMLMKAGADIAKKYAFPRLRFAASVGEPLNPEAVWWGKQVLGLPFHDNWWQTETGGIM 375

Query: 366 ICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNEL-----PPYRMGNLAIKKGWPSMMHTIW 420
           I N P  DIKPGSMG+P+PGVEAAIV  Q +        P + G LA+K+GWPSM     
Sbjct: 376 IANTPAFDIKPGSMGRPLPGVEAAIVSRQADGSVQVIEAPNKEGELALKRGWPSMFRGYL 435

Query: 421 NNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHP 480
           N+ E+Y   F  G WY++GD A  D +GY+WF GR DDVI ++G  +GPFEVES L+EHP
Sbjct: 436 NSEERYRKSF-SGEWYLTGDLARRDADGYYWFVGRADDVIKSAGHLIGPFEVESALMEHP 494

Query: 481 AIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKD 540
           A+AEA VIGKPDP+ GE++KAF++L  GFE S+ L+  +    +  L A  AP+EI F  
Sbjct: 495 AVAEAAVIGKPDPIAGEVVKAFVSLNNGFEQSEALRMALLGHARTRLGAAVAPKEIAFLT 554

Query: 541 KLPKTRSGKIMRRVLKAWELNLPAGDLSTME 571
           +LP+TRSGKIMRR+LKA EL LP GD ST+E
Sbjct: 555 QLPRTRSGKIMRRLLKARELGLPEGDTSTLE 585


Lambda     K      H
   0.318    0.136    0.425 

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: 997
Number of extensions: 58
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: 572
Length of database: 588
Length adjustment: 36
Effective length of query: 536
Effective length of database: 552
Effective search space:   295872
Effective search space used:   295872
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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