GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tctC in Klebsiella michiganensis M5al

Align TctC aka STM2786, component of The tricarboxylate transporter, TctABC (characterized)
to candidate BWI76_RS20035 BWI76_RS20035 hypothetical protein

Query= TCDB::Q9FA46
         (325 letters)



>FitnessBrowser__Koxy:BWI76_RS20035
          Length = 326

 Score =  554 bits (1428), Expect = e-163
 Identities = 275/326 (84%), Positives = 294/326 (90%), Gaps = 1/326 (0%)

Query: 1   MKKQLLRTLTASILLMST-SVLAQEAPSRTECIAPAKPGGGFDLTCKLIQVSLLETGAIE 59
           M    LR L+A  L + T S  A EAPSRTECIAPAKPGGGFDLTCKLIQVSL+ETGAI+
Sbjct: 1   MNIPFLRHLSALALCLCTASAWAVEAPSRTECIAPAKPGGGFDLTCKLIQVSLMETGAIK 60

Query: 60  KPMRVTYMPGGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLSQGKFGRYGVDDVRWLAS 119
           KPMRVTYMPGGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNL+QGKFGRYGVDDVRWLAS
Sbjct: 61  KPMRVTYMPGGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLAQGKFGRYGVDDVRWLAS 120

Query: 120 VGTDYGMIAVRADSPWKTLKDLMTAMEKDPNSVVIGAGASIGSQDWMKSALLAQKANVDP 179
           VGTDYGMIAVR DSPWK L   M AMEK+P S+VIGAGASIGSQDWMK+ALLAQKANVDP
Sbjct: 121 VGTDYGMIAVRTDSPWKNLPSFMAAMEKNPASIVIGAGASIGSQDWMKAALLAQKANVDP 180

Query: 180 HKMRYVAFEGGGEPVTALMGNHVQVVSGDLSEMVPYLGGDKIRVLAVFSENRLPGQLANI 239
           HKMRYVAFEGGGEPVTAL+GNHVQ VSGDLSEMVPYL G+KIRVLAVF+  RLPG LAN+
Sbjct: 181 HKMRYVAFEGGGEPVTALLGNHVQAVSGDLSEMVPYLQGNKIRVLAVFANERLPGALANV 240

Query: 240 PTAKEQGYDLVWPIIRGFYVGPKVSDADYQWWVDTFKKLQQTDEFKKQRDLRGLFEFDMT 299
           PTAKEQGYDLVWPIIRGF+VGPKVSDADYQWWVD F KLQQTD FKKQR+LRGLFEF+M 
Sbjct: 241 PTAKEQGYDLVWPIIRGFFVGPKVSDADYQWWVDEFTKLQQTDAFKKQRELRGLFEFNMN 300

Query: 300 GQQLDDYVKKQVTDYREQAKAFGLAK 325
           G++LD YVKKQV  YR+QAK+FGLAK
Sbjct: 301 GKELDAYVKKQVEAYRQQAKSFGLAK 326


Lambda     K      H
   0.318    0.135    0.401 

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: 496
Number of extensions: 13
Number of successful extensions: 1
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: 325
Length of database: 326
Length adjustment: 28
Effective length of query: 297
Effective length of database: 298
Effective search space:    88506
Effective search space used:    88506
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: 48 (23.1 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