GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-ABC in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1144 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__pseudo1_N1B4:Pf1N1B4_1144
          Length = 579

 Score =  438 bits (1126), Expect = e-127
 Identities = 233/518 (44%), Positives = 339/518 (65%), Gaps = 26/518 (5%)

Query: 125 MREEIRKQLLEAESEDAIIDIINQHDKDDDEEE----EEEEAAPAPAGKG--KILAVTAC 178
           M   + K++ ++    A+ D+     +  +E E     E  A PA A K   +++AVTAC
Sbjct: 69  MSRFVGKRVFQSTPAQALQDVEAVLRRGVEEAEVYVAPEVAAEPAAAVKSAPRLVAVTAC 128

Query: 179 PTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVAADKQVEM 238
           PTG+AHTFMAA+AL++ AK LG +++VET GS G ++ L+A+ I DA  +++AAD +V  
Sbjct: 129 PTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLSAEAIADADVVLLAADIEVAT 188

Query: 239 ERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEEAKGKSGSGIG 298
           ERF GK++ +      +++ +  + KA+ +       +G    A  +      K+G    
Sbjct: 189 ERFAGKKIYRCGTGIALKQAEATLNKALAEGKQESASTGAKGPAKQE------KTG---- 238

Query: 299 NTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAAALNFIGGDNALK 358
              YKHL++GVS MLP VV GG+++A+SF +GI +         T AAAL  IGGD A K
Sbjct: 239 --IYKHLLTGVSFMLPMVVAGGLMIALSFVFGITAFKEE----GTLAAALMQIGGDTAFK 292

Query: 359 LIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAGYVVILLKKVFTF 418
           L+V +LAG+IA SIADRPG APGM+GG +A+   AGF+GG+IAGF+AGY    + + +  
Sbjct: 293 LMVPLLAGYIAYSIADRPGLAPGMIGGLLASTLGAGFIGGIIAGFIAGYAAQAINR-YAR 351

Query: 419 IPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESLGTGNLVLMGIIL 478
           +PQSL+ LKP+LI PL     TG++M +VV  PVA  +  LT++L+S+GT N +L+G++L
Sbjct: 352 LPQSLEALKPILIIPLLASLFTGLVMIYVVGKPVAGMLAGLTHFLDSMGTTNAILLGVLL 411

Query: 479 GGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPPLGIALATTIFRNKFTQR 538
           GGMM +D+GGP+NKAA+ F + ++ + +YAP AA MA GMVPP+G+ +AT I R KF Q 
Sbjct: 412 GGMMCVDLGGPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIARRKFAQT 471

Query: 539 DREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLTEFFRVTLPAPHGGV 598
           +REAG     +G  F++EGAIPFAA DPLRVIPA++ G A+ G L+ +F   L APHGG+
Sbjct: 472 EREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGGL 531

Query: 599 FVAFI---TNHPMLYLLSIVIGAVVMAIILGIVKKPVT 633
           FV  I    NH +LYLL+IV G+++ A+   ++K+P T
Sbjct: 532 FVMLIPNAINHALLYLLAIVAGSLLTAVTYALLKRPET 569



 Score = 50.8 bits (120), Expect = 2e-10
 Identities = 29/103 (28%), Positives = 53/103 (51%), Gaps = 1/103 (0%)

Query: 171 KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIV 230
           K+  VTACP G+  + + A  L   A+  G    VE   ++  + +L+A  IE A  +++
Sbjct: 2   KLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVVDAAHPERQLSAATIEAAEWVLL 61

Query: 231 AADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIY 273
                V+M RF GKRV Q      ++  + ++ + + ++A +Y
Sbjct: 62  VTSAPVDMSRFVGKRVFQSTPAQALQDVEAVLRRGV-EEAEVY 103


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: 795
Number of extensions: 34
Number of successful extensions: 6
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: 579
Length adjustment: 37
Effective length of query: 598
Effective length of database: 542
Effective search space:   324116
Effective search space used:   324116
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