GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Caulobacter crescentus NA1000

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate CCNA_02490 CCNA_02490 3-ketoacyl-CoA thiolase

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



>FitnessBrowser__Caulo:CCNA_02490
          Length = 399

 Score =  248 bits (633), Expect = 2e-70
 Identities = 167/413 (40%), Positives = 228/413 (55%), Gaps = 33/413 (7%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59
           MT A I    RTPIG+ Y G+L+      L    ++  V R   +D   ++++V+G+A Q
Sbjct: 1   MTAAYICDGIRTPIGR-YGGSLSKVRADDLAAIPLKALVARNPSLDLAAIDEIVLGSANQ 59

Query: 60  QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119
            G    N+AR ALL AG PV+  G T++R CASGL+A+  AAR++     ++ + GG ES
Sbjct: 60  AGEDNRNVARMALLLAGYPVSVPGVTVNRLCASGLEAVGYAARAIASGHNDLVIAGGVES 119

Query: 120 IS---LVQNDKMNTFHA-------------VDPALEAIKGDVYMAMLDTAETVAKRYGIS 163
           +S    V     + F               V+PA+  + G    +M +TAE VA  YG++
Sbjct: 120 MSRAPFVMGKADSAFSRSAEIFDTTIGWRFVNPAMRKLYG--VDSMPETAENVATDYGVN 177

Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223
           RE QD ++L SQ RTAAAQ  G    EI P+     +  KA   +      + +DE PR 
Sbjct: 178 REDQDAFALRSQARTAAAQANGFLAGEITPVE----IPGKAGPTI------VDRDEHPR- 226

Query: 224 ETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSY 283
           ETT E LA LK +  EG T+TAGNAS ++DGA A VI S+      GL P     G  S 
Sbjct: 227 ETTMEALAKLKPIVREGGTVTAGNASGVNDGAVALVIASEDAVKRHGLTPRARITGYASA 286

Query: 284 GCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNV 341
           G EP  MGIGPV AV +L+ + GL++ D  + ELNEAFA Q L    +LG+  D   +N 
Sbjct: 287 GVEPRVMGIGPVPAVRKLMAKTGLAIGDFDVVELNEAFAAQGLAVLRQLGLPDDGAHVNA 346

Query: 342 NGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           NGGAI++GHP G SGARL   AL +      +  + T+C+G G G+A  FE V
Sbjct: 347 NGGAIALGHPLGASGARLVLTALRQLEASGGQRGLATLCIGVGQGAALAFERV 399


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: 434
Number of extensions: 33
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: 395
Length of database: 399
Length adjustment: 31
Effective length of query: 364
Effective length of database: 368
Effective search space:   133952
Effective search space used:   133952
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