GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Halomonas xinjiangensis TRM 0175

Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= TCDB::O30494
         (367 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  321 bits (823), Expect = 2e-92
 Identities = 171/358 (47%), Positives = 243/358 (67%), Gaps = 21/358 (5%)

Query: 1   MANLKIKNLQKGFEG-FSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGT 59
           MA++++  L+K + G    +KGIDLE+ D EFVV VGPSGCGKSTLLR++AGLE +++GT
Sbjct: 1   MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60

Query: 60  IELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAAR 119
           +++D R + ++ PA+RD+AMVFQ YALYPHM+V  N+++ L   GV ++ +E +V++AA 
Sbjct: 61  LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120

Query: 120 ILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARL 179
           +LE+ P LERKP++LSGGQRQRVA+GRA+VR P  FLFDEPLSNLDA LRVQMR+E+ +L
Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180

Query: 180 HKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKM 239
            + L+ T +YVTHDQ+EA+TL D++VVLN G IEQVG+P+E+Y +PA++FVA F+G+P M
Sbjct: 181 QRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAM 240

Query: 240 GFLKGKVTRVDG-QGCEVQLDAGTLISLPLSGASLSVGSAVTLGIRPEHLEIASPGQTTL 298
             L     R  G  G    L A T +                +GIRP+ L I +P +  L
Sbjct: 241 NMLPVAYLRERGANGLLDHLAADTDV----------------IGIRPDDLRIEAPDEDHL 284

Query: 299 TVTADVG--ERLGSDTFCHV-ITSNGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFD 353
            VT  V   E  G+++  +V +  + +P  +R         GET+  H+ P+  H F+
Sbjct: 285 VVTGTVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPFN 342


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: 361
Number of extensions: 12
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: 354
Length adjustment: 29
Effective length of query: 338
Effective length of database: 325
Effective search space:   109850
Effective search space used:   109850
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 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