GapMind for catabolism of small carbon sources

 

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

Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate H281DRAFT_05701 H281DRAFT_05701 glycerol 3-phosphate ABC transporter ATP-binding protein

Query= TCDB::O30494
         (367 letters)



>FitnessBrowser__Burk376:H281DRAFT_05701
          Length = 362

 Score =  358 bits (920), Expect = e-103
 Identities = 196/363 (53%), Positives = 254/363 (69%), Gaps = 19/363 (5%)

Query: 1   MANLKIKNLQKGFEGFS-IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGT 59
           MA L ++ ++K ++G   ++ GID++VND EFVV VGPSGCGKSTLLR++AGLE +SEGT
Sbjct: 1   MAALTLQGVKKTYDGKQFVLHGIDVDVNDGEFVVMVGPSGCGKSTLLRMVAGLERISEGT 60

Query: 60  IELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAAR 119
           I + G+ + E+ P  R++AMVFQ YALYPHMSV +NM +AL +AGVD+  +  +VN AA+
Sbjct: 61  ISIAGKVVNELEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAQRVNAAAQ 120

Query: 120 ILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARL 179
           ILEL PLL+RKP++LSGGQRQRVA+GRAIVR P +FLFDEPLSNLDA LRVQMRLE+ RL
Sbjct: 121 ILELEPLLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQRL 180

Query: 180 HKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKM 239
           H  L  T +YVTHDQ+EAMTLA +V+V+N G  EQ+G+P E+Y +PA +FVAGF+G+P M
Sbjct: 181 HARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVAGFIGSPGM 240

Query: 240 GFLKGKVTRVDGQGCEVQLDAGTLISLPLSGASLSVGSAV------TLGIRPEHLEIASP 293
             L+G+V+  DG   +V   AG    LPL+G + S+G  V      TLGIRPEH+   SP
Sbjct: 241 NLLEGRVSD-DGSTFDV---AGNGPQLPLAGVA-SIGREVAKGREWTLGIRPEHM---SP 292

Query: 294 GQTT---LTVTADVGERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLDPAHCH 350
           GQ      T+T D  E LG+D   H      + +T R+        GE L + L   H H
Sbjct: 293 GQADAPHTTLTVDSCELLGADNLAHGRWGKHD-VTARLPHAHRPAAGEALQVALPARHLH 351

Query: 351 LFD 353
            FD
Sbjct: 352 FFD 354


Lambda     K      H
   0.319    0.137    0.387 

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: 413
Number of extensions: 17
Number of successful extensions: 3
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: 367
Length of database: 362
Length adjustment: 29
Effective length of query: 338
Effective length of database: 333
Effective search space:   112554
Effective search space used:   112554
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