GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-ABC in Pseudomonas fluorescens FW300-N2E2

Align The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized)
to candidate Pf6N2E2_3337 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)

Query= TCDB::P71012
         (635 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3337
          Length = 575

 Score =  429 bits (1102), Expect = e-124
 Identities = 227/517 (43%), Positives = 339/517 (65%), Gaps = 27/517 (5%)

Query: 125 MREEIRKQLLEAESEDAIIDIINQHDKDDDEEE-----EEEEAAPAPAGKG--KILAVTA 177
           M   + K+L  +    A+ D+ +   +  +E E     +  E APA +     +++A+TA
Sbjct: 64  MSRFVGKRLFRSTPALALQDVDSVLRRGAEEAEVFLASDVVEQAPAVSTDRAPRLVAITA 123

Query: 178 CPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVAADKQVE 237
           CPTG+AHTFMAA+AL++ A +LG +++VET GS G ++ L+A+ I +A  +++A D +V 
Sbjct: 124 CPTGVAHTFMAAEALQQAATKLGYDLQVETQGSVGARNPLSAEAIAEADVVLLATDIEVA 183

Query: 238 MERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEEAKGKSGSGI 297
            ERF GK++ +      +++ +  + KA+ +       SG  + A ++      K+G   
Sbjct: 184 TERFAGKKIYRCSTGIALKQAEATLNKALVEGRQESASSGASAPAKSE------KTG--- 234

Query: 298 GNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAAALNFIGGDNAL 357
               YKHL++GVS MLP VV GG+++A+SF +GI +    +P   T AAAL  IGGD A 
Sbjct: 235 ---VYKHLLTGVSFMLPMVVAGGLMIALSFVFGIEAF--KEPG--TLAAALMQIGGDTAF 287

Query: 358 KLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAGYVVILLKKVFT 417
           KL+V +LAG+IA SIADRPG APGM+GG +A+   AGF+GG+IAGFLAGY    + + + 
Sbjct: 288 KLMVPLLAGYIAYSIADRPGLAPGMIGGMLASTLGAGFIGGIIAGFLAGYAAKAISR-YA 346

Query: 418 FIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESLGTGNLVLMGII 477
            +PQSL+ LKP+LI PL     TG++M ++V  PVA  +  LT++L+S+GT N +L+G++
Sbjct: 347 RLPQSLEALKPILIIPLLASLFTGLVMIYIVGKPVAGMLEALTHFLDSMGTTNAILLGVL 406

Query: 478 LGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPPLGIALATTIFRNKFTQ 537
           LG MM +D+GGP+NKAA+ F + ++ + +YAP AA MA GMVPP+G+ +AT I R KF Q
Sbjct: 407 LGAMMCVDLGGPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIARRKFAQ 466

Query: 538 RDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLTEFFRVTLPAPHGG 597
            +REAG     +G  F++EGAIPFAA DPLRVIPA++ G A+ G L+ +F   L APHGG
Sbjct: 467 TEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGG 526

Query: 598 VFVAFI---TNHPMLYLLSIVIGAVVMAIILGIVKKP 631
           +FV  I    NH +LYLL+IV G+++  +   ++K+P
Sbjct: 527 LFVMLIPNAINHALLYLLAIVAGSLLTGVAYALLKRP 563



 Score = 46.2 bits (108), Expect = 4e-09
 Identities = 24/74 (32%), Positives = 41/74 (55%)

Query: 175 VTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVAADK 234
           VTACP G+  + + A  L   A+  G    VE + ++  + +L+A  +E A  +++ A  
Sbjct: 1   VTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEAAEWVLLVASG 60

Query: 235 QVEMERFKGKRVLQ 248
            V+M RF GKR+ +
Sbjct: 61  PVDMSRFVGKRLFR 74


Lambda     K      H
   0.320    0.137    0.390 

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: 780
Number of extensions: 34
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 635
Length of database: 575
Length adjustment: 37
Effective length of query: 598
Effective length of database: 538
Effective search space:   321724
Effective search space used:   321724
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: 53 (25.0 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