GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Pseudomonas fluorescens GW456-L13

Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate PfGW456L13_4298 D-glycerate 2-kinase (EC 2.7.1.-)

Query= reanno::psRCH2:GFF1145
         (423 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4298
          Length = 426

 Score =  668 bits (1724), Expect = 0.0
 Identities = 337/419 (80%), Positives = 377/419 (89%)

Query: 1   MTLDPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEG 60
           M++DPQ LLR+LF +AI+AAHP+ VL  HLP DRSGR IVIGAGKAAAAMA+ +E+ W+G
Sbjct: 1   MSVDPQQLLRELFATAIDAAHPQQVLEAHLPADRSGRVIVIGAGKAAAAMAQVVERCWQG 60

Query: 61  ELSGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGG 120
           E+SGLVVTRY H A C++IEVVEAAHPVPD AG  VA+RVLELVS+L ESDRVIFLLSGG
Sbjct: 61  EVSGLVVTRYGHGAPCEKIEVVEAAHPVPDAAGLAVAKRVLELVSDLNESDRVIFLLSGG 120

Query: 121 GSSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYT 180
           GS+LLALPAEGI+LADKQ+INKALL+SGA IGEMNCVRKHLSAIKGGRL KACWPA+VYT
Sbjct: 121 GSALLALPAEGITLADKQSINKALLKSGATIGEMNCVRKHLSAIKGGRLGKACWPATVYT 180

Query: 181 YAISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGD 240
           YAISDVPGD ATVIASGPTVADP+TS +AL IL+RY IEVPA+VRAWL+ P SET+KPGD
Sbjct: 181 YAISDVPGDLATVIASGPTVADPSTSAEALAILKRYAIEVPASVRAWLQSPESETVKPGD 240

Query: 241 PMLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGDLEGEAREVAKVHAGIARQVVLHG 300
           P L+RSHF+LIA PQQSL+AAA   R AG +PLILGDLEGE+REVAKVHAGIARQ+VLHG
Sbjct: 241 PSLARSHFQLIARPQQSLEAAAVKCRQAGFSPLILGDLEGESREVAKVHAGIARQIVLHG 300

Query: 301 QPIAAPCVILSGGETTVTVRGNGRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGSED 360
           QP+AAPCVILSGGETTVTVRGNGRGGRNAEFLL+LT++L+GLP VYALAGDTDGIDGSED
Sbjct: 301 QPLAAPCVILSGGETTVTVRGNGRGGRNAEFLLSLTDSLKGLPGVYALAGDTDGIDGSED 360

Query: 361 NAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILIL 419
           NAGA+M PDSYARA   GL A+D L NN+GYGYF ALD LIVT PTRTNVNDFRAILIL
Sbjct: 361 NAGAIMTPDSYARAAAKGLSASDELDNNNGYGYFEALDALIVTEPTRTNVNDFRAILIL 419


Lambda     K      H
   0.316    0.134    0.384 

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: 577
Number of extensions: 18
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: 423
Length of database: 426
Length adjustment: 32
Effective length of query: 391
Effective length of database: 394
Effective search space:   154054
Effective search space used:   154054
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 (21.6 bits)
S2: 51 (24.3 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