GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Sinorhizobium meliloti 1021

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate SM_b20589 SM_b20589 beta-ketoadipyl CoA thiolase

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



>FitnessBrowser__Smeli:SM_b20589
          Length = 400

 Score =  240 bits (612), Expect = 6e-68
 Identities = 163/413 (39%), Positives = 225/413 (54%), Gaps = 32/413 (7%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59
           M EA I    RTPIG+ + G+L +     L    ++  + R   +D + V+DV+ G A Q
Sbjct: 1   MREAYICDYIRTPIGR-FGGSLASVRADDLGAIPLKALMDRNRSVDWEAVDDVIFGCANQ 59

Query: 60  QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119
            G    NIAR +LL AGLPV   GTTI+R C SG+ A+  AAR++     E+ + GG ES
Sbjct: 60  AGEDNRNIARMSLLLAGLPVAVPGTTINRLCGSGMDAVIAAARAIKCGEAELMIAGGVES 119

Query: 120 ISLVQ----------------NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGIS 163
           +S                    D    +  V+P ++A  G    +M +T E VA+ Y +S
Sbjct: 120 MSRAPFVLPKAESAFSRNAEIYDTTIGWRFVNPLMKAQYG--VDSMPETGENVAEDYKVS 177

Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223
           RE QD ++L SQ + AAAQ  G+   EI  ++     + +  G      + + +DE PR 
Sbjct: 178 REDQDAFALRSQAKAAAAQANGRLASEIVAVT-----IPQRKGG----PVVIDRDEHPRA 228

Query: 224 ETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSY 283
            TT E LAGLK    EG T+TAGNAS ++DGA+A +I S++ A   GL+P+    G  S 
Sbjct: 229 -TTIEALAGLKTPFREGGTVTAGNASGVNDGAAALIIASEEAARKHGLRPMARILGGASA 287

Query: 284 GCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNV 341
           G  P  MG+GPV A  RL+ R G + D   + ELNEAFA Q L     LGI  D  ++N 
Sbjct: 288 GVPPRIMGMGPVPASQRLMTRLGATQDRFDVIELNEAFASQGLAVLRALGIADDDPRVNR 347

Query: 342 NGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           NGGAI++GHP GMSGAR+ G A +E      + ++ TMC+G G G A   E V
Sbjct: 348 NGGAIALGHPLGMSGARITGTAALELAETGGRTSLSTMCIGVGQGIAVALERV 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: 425
Number of extensions: 26
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: 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