GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3337 PTS system,
           fructose-specific IIB component (EC 2.7.1.69) / PTS
           system, fructose-specific IIC component (EC 2.7.1.69)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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