GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Mesorhizobium ciceri WSM1271

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate YP_004140309.1 Mesci_1095 beta-ketoadipyl CoA thiolase

Query= SwissProt::Q0AVM3
         (396 letters)



>NCBI__GCF_000185905.1:YP_004140309.1
          Length = 401

 Score =  336 bits (862), Expect = 6e-97
 Identities = 181/400 (45%), Positives = 260/400 (65%), Gaps = 12/400 (3%)

Query: 4   EVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL 62
           E  +    RTP+G FGG+L  V S  LGAI +    +R  GI  + ID+V++GC  QAG 
Sbjct: 3   EAYICDYIRTPIGRFGGSLSSVRSDDLGAIPLRALAERNPGIDWQAIDDVVYGCANQAGE 62

Query: 63  -GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDK 121
             +NVAR  ++ AG+PKEV   T+N++CGSG+ A+++AA+ IKAG+A++++AGG E+M +
Sbjct: 63  DNRNVARMALLLAGLPKEVPGSTVNRLCGSGMDALTIAARAIKAGEAELMIAGGVESMSR 122

Query: 122 APFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYHMGI-----TAENINDMYGITRE 176
           APF++P A   +  +    ++ D  +     +       G+     T EN+ + + ++R 
Sbjct: 123 APFVMPKADTAFSRN---AEIYDTTIGWRFVNPLMKKQYGVDSMPETGENVAEDFSVSRA 179

Query: 177 EQDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGD-IVFDTDEHPRK-STPEAMAKLA 234
           +QDAF  RSQ  A  A  +GR   EI PV I  +KGD ++   DEHPR  ST EA+AKL 
Sbjct: 180 DQDAFAVRSQNKAVAAQANGRLAKEITPVTILQRKGDALIVSKDEHPRAGSTVEALAKLP 239

Query: 235 PAFKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGP 294
             F++GG+VTAGNASG+ND AAA+IV S+    + G+ P+A+++  A+ GV P +MG+GP
Sbjct: 240 TPFRQGGTVTAGNASGVNDGAAALIVASEAAVKKYGLTPIARILGGAAAGVAPRIMGIGP 299

Query: 295 IPASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPI 354
           +PA++K   + GLT    D+IE NEAFA+Q IAV R LG A+  E VN NGGAIA+GHP+
Sbjct: 300 VPATQKLCARLGLTPKQFDVIELNEAFASQGIAVLRQLGIAEDAEHVNPNGGAIALGHPL 359

Query: 355 GSSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
           G SGARI  T   E+++RG +  LAT+CIG G G A+ +E
Sbjct: 360 GMSGARISGTAALELRERGGRYALATMCIGVGQGIAIALE 399


Lambda     K      H
   0.317    0.135    0.387 

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: 491
Number of extensions: 26
Number of successful extensions: 6
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: 396
Length of database: 401
Length adjustment: 31
Effective length of query: 365
Effective length of database: 370
Effective search space:   135050
Effective search space used:   135050
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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