GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate H281DRAFT_00169 H281DRAFT_00169 carbohydrate ABC transporter ATP-binding protein, CUT1 family

Query= reanno::WCS417:GFF4321
         (386 letters)



>FitnessBrowser__Burk376:H281DRAFT_00169
          Length = 371

 Score =  417 bits (1073), Expect = e-121
 Identities = 225/371 (60%), Positives = 277/371 (74%), Gaps = 7/371 (1%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           MA+L +R+V KTY  G+P  LK + + I++G+FLILVG SGCGKSTL+N IAGLET+T G
Sbjct: 1   MASLSIRDVYKTYPNGVP-VLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKG 59

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            I I  + V+ +SPKDRDIAMVFQSYALYP+M+VRENI FGL IRK+P+ +    V RV+
Sbjct: 60  EIQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRKVPKQEQAQIVDRVS 119

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
             LQI HLL+RKPGQLSGGQ+QRVAMGRALAR P ++LFDEPLSNLDAKLR+EMR+E+KL
Sbjct: 120 NTLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRSEIKL 179

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
           +HQRL TT VYVTHDQIEAMTLGD++AVMKDGI+QQFG P+EIY++P+N FVA FIG+PP
Sbjct: 180 LHQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGFIGAPP 239

Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLED---RDVILGLRPEQIMLAAG- 296
           MNF+  +L  +   +   LD+G  R  L L    A ++    R+VILGLRPE+I  A G 
Sbjct: 240 MNFIQGKLVEQGAGVGIELDTGVTRTALNLPFDSAKVKSHVGREVILGLRPERITDARGA 299

Query: 297 EGDSA--SSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKV 354
            GD A    I  +V V EPTGPDTLVF Q+N  +V  R+ P   PQ     TL FD SK 
Sbjct: 300 HGDHARLQQIEVKVDVIEPTGPDTLVFAQVNGKRVVSRVHPASNPQPLTNTTLLFDTSKA 359

Query: 355 LLFDANTGERL 365
           +LFD +  ER+
Sbjct: 360 VLFDPSNEERI 370


Lambda     K      H
   0.318    0.135    0.382 

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: 442
Number of extensions: 16
Number of successful extensions: 4
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: 371
Length adjustment: 30
Effective length of query: 356
Effective length of database: 341
Effective search space:   121396
Effective search space used:   121396
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: 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