GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Klebsiella michiganensis M5al

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate BWI76_RS17830 BWI76_RS17830 ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__Koxy:BWI76_RS17830
          Length = 364

 Score =  324 bits (830), Expect = 3e-93
 Identities = 177/374 (47%), Positives = 250/374 (66%), Gaps = 25/374 (6%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           M ++ L +V K+YG      +K++ L I DGEF +LVGPSGCGKSTL+  IAGLE ISGG
Sbjct: 1   MGSVVLNSVRKSYGDA--HVIKDVSLTIPDGEFCVLVGPSGCGKSTLLRMIAGLEEISGG 58

Query: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120
            + +++ +++ + PK RDIAMVFQSYALYP M+VR+N+ F LK+ K+P AEI+++V   +
Sbjct: 59  EVHINERNVTEVEPKLRDIAMVFQSYALYPQMTVRENMGFALKMAKLPKAEINQKVNEAA 118

Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
            LL +E LL R P  LSGGQ+QRVAMGRA+ R+P+++LFDEPLSNLDAKLR ++R E++ 
Sbjct: 119 ALLGLEPLLERLPKDLSGGQRQRVAMGRAIVRKPQVFLFDEPLSNLDAKLRTQVRGEIRE 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240
           +H+RLKTT+VYVTHDQIEAMT+G  + V++DG I+Q GTP ++Y+ PANLFVA FIGSP 
Sbjct: 179 LHRRLKTTSVYVTHDQIEAMTMGQMIVVLRDGRIEQAGTPLELYDRPANLFVAGFIGSPE 238

Query: 241 MNFIP---------LRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQI 291
           +N +P           L+ KDG LLA          LP G++    + ++V+  IRPEQ+
Sbjct: 239 INQLPGEVVLNGNATSLRLKDGSLLA----------LPAGLRVT--DGQQVVYAIRPEQV 286

Query: 292 ILANGEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDP 351
            + +   +    + A+V   E TG D  +F +             +A   G+ + LQ   
Sbjct: 287 NVVHEARD--DALAAKVTAVENTGSDMQLFCDTGGGAFTSVFKQRLAVKEGDKIWLQPKL 344

Query: 352 AKVLLFDAKTGERL 365
           + V LFDA++G+R+
Sbjct: 345 SGVHLFDAQSGQRI 358


Lambda     K      H
   0.319    0.138    0.393 

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: 427
Number of extensions: 18
Number of successful extensions: 2
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: 386
Length of database: 364
Length adjustment: 30
Effective length of query: 356
Effective length of database: 334
Effective search space:   118904
Effective search space used:   118904
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 (21.7 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