GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Klebsiella michiganensis M5al

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>FitnessBrowser__Koxy:BWI76_RS16135
          Length = 400

 Score =  245 bits (626), Expect = 1e-69
 Identities = 160/413 (38%), Positives = 230/413 (55%), Gaps = 32/413 (7%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59
           M +A I    RTP G+ + G L       L    ++  ++R  G+DP  ++DV+ G A Q
Sbjct: 1   MNQAFICDAVRTPFGR-FGGTLATLRADDLAALPLKALLERNPGLDPARIDDVIYGCANQ 59

Query: 60  QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119
            G    N+AR ALL AGLP +  G+T++R C S L AI +AAR++     ++ + GG ES
Sbjct: 60  AGEDNRNVARMALLLAGLPESVPGSTVNRLCGSSLDAIGIAARAIKSGETQLMIAGGVES 119

Query: 120 IS----------------LVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGIS 163
           +S                +   D    +  ++P ++A+ G    +M +TAE VA  + IS
Sbjct: 120 MSRAPFVMGKAESAFSRTMRMEDTTIGWRFINPQMKALYG--VDSMPETAENVADDFAIS 177

Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223
           R  QD ++L SQ RTAAAQ+ G+F DE+  +S     V +  G    + +  S+DE PR 
Sbjct: 178 RADQDAFALRSQLRTAAAQEAGRFADELIAVS-----VPQRKG----EPLLFSRDEHPRT 228

Query: 224 ETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSY 283
            TTAE LA L+ V     T+TAGNAS ++DGA A ++ S++  AA  L+PL    G+ + 
Sbjct: 229 -TTAEALARLRGVVRPDGTVTAGNASGVNDGACALLLASEQALAANDLQPLARVVGVATA 287

Query: 284 GCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNV 341
           G  P  MG GP  AV ++L + GL++  + + ELNEAFA Q L     LG+  D   +N 
Sbjct: 288 GVAPRIMGFGPAPAVRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDDAAYVNP 347

Query: 342 NGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           NGGAI++GHP G SG RLA  A  + RR   +YA+ TMC+G G G A + E V
Sbjct: 348 NGGAIALGHPLGASGGRLAMTAAYQLRRTGGRYALCTMCIGVGQGIALIIERV 400


Lambda     K      H
   0.316    0.134    0.378 

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: 400
Number of extensions: 21
Number of successful extensions: 4
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: 395
Length of database: 400
Length adjustment: 31
Effective length of query: 364
Effective length of database: 369
Effective search space:   134316
Effective search space used:   134316
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: 50 (23.9 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