GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Pseudomonas fluorescens FW300-N2C3

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate AO356_27685 AO356_27685 ABC transporter ATP-binding protein

Query= reanno::psRCH2:GFF857
         (371 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27685
          Length = 367

 Score =  375 bits (963), Expect = e-108
 Identities = 192/368 (52%), Positives = 256/368 (69%), Gaps = 1/368 (0%)

Query: 1   MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60
           MA++ ++++ K ++G  I + IDL++ D EFVVFVGPSGCGKSTLLRLIAGLE+++ G +
Sbjct: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVSDGTI 60

Query: 61  LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120
            +D + + ++ P  R + MVFQ+YALYPHM+V +NM+F L LA V K E++++V   A I
Sbjct: 61  ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVPKAEVEKKVNEAARI 120

Query: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180
           L+L  +LERKPK LSGGQRQRVAIGR +VR PK+FLFDEPLSNLDA LRVQMR+E+ARLH
Sbjct: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180

Query: 181 QRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMN 240
           + +++TMIYVTHDQVEAMTLADK+VVLN G I QVG PL LYH P N FVAGFLG+P+M 
Sbjct: 181 KELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240

Query: 241 FVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEADFTFHG 300
           F++ +  +   +   + L +G  + LP  G+ +S G  +TLGIRPEH  +    D T   
Sbjct: 241 FLKGKVTALDSQGCEVLLDAGTRINLPRSGANLSVGGAVTLGIRPEHLNLAQPGDCTLQV 300

Query: 301 QITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRENGEAC 360
              V+ERLG     ++ +    + +T+ V G+L    GE     L A+ CHLF   G A 
Sbjct: 301 TADVSERLGSDTFCHV-VTTSGEALTMRVRGDLASRFGEQLNLHLDAEHCHLFDAEGVAV 359

Query: 361 TRHYREPA 368
           +R  R  A
Sbjct: 360 SRALRAAA 367


Lambda     K      H
   0.322    0.139    0.405 

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: 416
Number of extensions: 13
Number of successful extensions: 2
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: 371
Length of database: 367
Length adjustment: 30
Effective length of query: 341
Effective length of database: 337
Effective search space:   114917
Effective search space used:   114917
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 (21.9 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