GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galT in Klebsiella michiganensis M5al

Align UDP-glucose-hexose-1-phosphate uridylyltransferase (EC 2.7.7.12) (characterized)
to candidate BWI76_RS08620 BWI76_RS08620 galactose-1-phosphate uridylyltransferase

Query= BRENDA::P09148
         (348 letters)



>FitnessBrowser__Koxy:BWI76_RS08620
          Length = 348

 Score =  685 bits (1768), Expect = 0.0
 Identities = 321/348 (92%), Positives = 331/348 (95%)

Query: 1   MTQFNPVDHPHRRYNPLTGQWILVSPHRAKRPWQGAQETPAKQVLPAHDPDCFLCAGNVR 60
           M+ FNPVDHPHRRYNPLTGQWILVSPHRAKRPWQGAQETPAKQ LPAHDPDCFLC GN R
Sbjct: 1   MSVFNPVDHPHRRYNPLTGQWILVSPHRAKRPWQGAQETPAKQSLPAHDPDCFLCPGNTR 60

Query: 61  VTGDKNPDYTGTYVFTNDFAALMSDTPDAPESHDPLMRCQSARGTSRVICFSPDHSKTLP 120
           VTGDKNP+YTGT+VFTNDFAALM+DTPDAPES DPLMRCQSARGTSRVICFSPDHSKTLP
Sbjct: 61  VTGDKNPNYTGTFVFTNDFAALMTDTPDAPESDDPLMRCQSARGTSRVICFSPDHSKTLP 120

Query: 121 ELSVAALTEIVKTWQEQTAELGKTYPWVQVFENKGAAMGCSNPHPHGQIWANSFLPNEAE 180
           ELSV AL  +VKTWQEQTA+LGKTYPWVQVFENKGAAMGCSNPHPHGQ+WANSFLPNEAE
Sbjct: 121 ELSVEALEGVVKTWQEQTADLGKTYPWVQVFENKGAAMGCSNPHPHGQVWANSFLPNEAE 180

Query: 181 REDRLQKEYFAEQKSPMLVDYVQRELADGSRTVVETEHWLAVVPYWAAWPFETLLLPKAH 240
           REDRLQK YF E  +PMLVDY QRELADGSRTVVETEHWLAVVPYWAAWPFETLLLPKAH
Sbjct: 181 REDRLQKAYFTEHGAPMLVDYAQRELADGSRTVVETEHWLAVVPYWAAWPFETLLLPKAH 240

Query: 241 VLRITDLTDAQRSDLALALKKLTSRYDNLFQCSFPYSMGWHGAPFNGEENQHWQLHAHFY 300
           V R+TDLTD QRSDLALALKKLTSRYDNLFQCSFPYSMGWHGAPFN EEN HWQLHAHFY
Sbjct: 241 VQRLTDLTDDQRSDLALALKKLTSRYDNLFQCSFPYSMGWHGAPFNDEENNHWQLHAHFY 300

Query: 301 PPLLRSATVRKFMVGYEMLAETQRDLTAEQAAERLRAVSDIHFRESGV 348
           PPLLRSATVRKFMVGYEMLAETQRDLTAEQAAERLRAVSD+HFRESGV
Sbjct: 301 PPLLRSATVRKFMVGYEMLAETQRDLTAEQAAERLRAVSDVHFRESGV 348


Lambda     K      H
   0.319    0.133    0.425 

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: 649
Number of extensions: 19
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: 348
Length of database: 348
Length adjustment: 29
Effective length of query: 319
Effective length of database: 319
Effective search space:   101761
Effective search space used:   101761
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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