GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Tatumella morbirosei LMG 23360

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_038017589.1 HA49_RS11785 maltose/maltodextrin ABC transporter ATP-binding protein MalK

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



>NCBI__GCF_000757425.2:WP_038017589.1
          Length = 369

 Score =  294 bits (753), Expect = 2e-84
 Identities = 164/360 (45%), Positives = 231/360 (64%), Gaps = 10/360 (2%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           MA++ L  V K+YG  +    ++I L I+EGEF++LVGPSGCGKST++  IAGLE IT G
Sbjct: 1   MASVSLDGVYKSYGETVIS--RDITLEIEEGEFVVLVGPSGCGKSTILRMIAGLEDITAG 58

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            + I  Q ++   P DR I MVFQSYALYP ++V EN+ FGLK+    +++I   V +VA
Sbjct: 59  ELKIAGQRMNETPPADRGIGMVFQSYALYPHLTVAENMSFGLKLAGTKKSEIAQRVNQVA 118

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           ++LQ+ HLL+R+P  LSGGQ+QRVA+GR L   P ++L DEPLSNLDA LRV+MR E+  
Sbjct: 119 EVLQLAHLLDRRPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISR 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
           +H+RLK T +YVTHDQ+EAMTL DK+ V+  G I Q G P  +Y+ PAN+FVA FIGSP 
Sbjct: 179 LHKRLKRTMIYVTHDQVEAMTLADKIVVLDAGQIAQIGKPLALYHYPANRFVAGFIGSPK 238

Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300
           MNF+P++    + R V +    + R  L +   +      ++ LG+RPE ++     GD+
Sbjct: 239 MNFLPVKATAAEARRVEVELPNRQRIWLMVEGHDI-TPGSNLSLGIRPEHLL----PGDA 293

Query: 301 AS-SIRAEVQVTEPTGPDTLVFVQLNDTK--VCCRLAPDVAPQVGETLTLQFDPSKVLLF 357
           A  ++  EVQV E  G +T + +Q+   +  +  R    V  + G T T+   P +  LF
Sbjct: 294 AEVTLSGEVQVAERLGNETQIHIQIPAIRQNLVYRQNDVVLAEEGATFTIGLPPHRCHLF 353


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: 360
Number of extensions: 14
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: 386
Length of database: 369
Length adjustment: 30
Effective length of query: 356
Effective length of database: 339
Effective search space:   120684
Effective search space used:   120684
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 24 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