GapMind for catabolism of small carbon sources

 

Alignments 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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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