GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Pseudomonas fluorescens FW300-N2E3

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate AO353_25895 AO353_25895 ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25895
          Length = 367

 Score =  326 bits (835), Expect = 7e-94
 Identities = 170/367 (46%), Positives = 241/367 (65%), Gaps = 17/367 (4%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           MA + ++++ K + G +   +K  +L++ D+EF VFVGPSGCGK+T LR+IAGLE++T G
Sbjct: 1   MAHLKIKNLQKGFEGFS--IIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAG 58

Query: 61  NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120
            + +  R + +V P  RD+AMVFQ YALYPHM+V +NM+F L L  V KAE++++V EAA
Sbjct: 59  TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAA 118

Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180
           +IL++  +L+RKPK LSGGQRQRVA+GRAIVR P++FL DEPLSNLDA LRVQMR E+ +
Sbjct: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELAR 178

Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240
           LH+ LQ T+IYVTHDQ EAMT+ D++VV+  G I+Q  +P  +Y QP N+FVAGF+G+P 
Sbjct: 179 LHKELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPK 238

Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGA---IGKPVVLGVRPEDLHDEE 297
           M F++G++ +          +  + L  G    L  SGA   IG  V LG+RPE L+   
Sbjct: 239 MGFLKGKVTR------VERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLN--- 289

Query: 298 VFMTTYPDSVLQMQVEVVEHMGSEVYLHT-SIGPNTIVARVNPRHVYHVGSSVKLAIDLN 356
             +    D  LQ+  +V E +GS+ + H  +     +  R+        G  + L +D  
Sbjct: 290 --LALPGDCTLQVTADVSERLGSDTFCHVLTASGEALTMRIRGDLASRYGEQLSLHLDAE 347

Query: 357 KIHIFDA 363
             H+FDA
Sbjct: 348 HCHLFDA 354


Lambda     K      H
   0.321    0.138    0.395 

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: 402
Number of extensions: 14
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: 384
Length of database: 367
Length adjustment: 30
Effective length of query: 354
Effective length of database: 337
Effective search space:   119298
Effective search space used:   119298
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: 50 (23.9 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