GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruI in Pseudomonas stutzeri RCH2

Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate GFF3289 Psest_3353 PTS system, fructose-specific, IIB component/PTS system, fructose subfamily, IIC component

Query= TCDB::Q1LZ59
         (655 letters)



>lcl|FitnessBrowser__psRCH2:GFF3289 Psest_3353 PTS system,
           fructose-specific, IIB component/PTS system, fructose
           subfamily, IIC component
          Length = 579

 Score =  335 bits (859), Expect = 3e-96
 Identities = 195/489 (39%), Positives = 288/489 (58%), Gaps = 45/489 (9%)

Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228
           LVAVTAC TG+AHT+MA EAL++ A   G  ++VET G+ G  N L AD I  A  V++A
Sbjct: 120 LVAVTACPTGVAHTFMAAEALQQAAIRKGYDLQVETRGSVGARNVLEADVIAAADVVLLA 179

Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKAG 288
           AD  V++ RF GK +        +K+PE  ++  L+   E  V   + +++ AS  EK G
Sbjct: 180 ADIEVDVARFAGKRVFRCGTGVALKQPEATLDRALE---EGAVLSGNAVATSASG-EKKG 235

Query: 289 LGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQV 348
             +  YKH+++GVS MLP V+ GG++IALSF+        + +L+        AA+    
Sbjct: 236 EKTGVYKHMLTGVSYMLPMVVAGGLLIALSFVFGIEAFKEEGTLA--------AALMKIG 287

Query: 349 GNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLT 408
           G  AF  M+P+ A YIAYSIA++PGL  G + G +A T                      
Sbjct: 288 GETAFQLMVPLLAGYIAYSIADRPGLAPGMIGGLLAGT---------------------- 325

Query: 409 GIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLF-VN 467
            + +GF+G +  GF+AG     + + +  +P S+E +K IL+ PLL  LVTG +M++ V 
Sbjct: 326 -LGAGFIGGIIAGFVAGYAAKAVSRWIP-LPASIESLKPILIIPLLASLVTGLVMIYIVG 383

Query: 468 IPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALAK 527
            P+A +   L  FL  +   +A+LLGL++G MM +D+GGP NKAAY F    L + + A 
Sbjct: 384 TPVAKLLAGLTEFLDTMGTSNAILLGLLLGTMMCVDLGGPVNKAAYAFSVGLLASQSYAP 443

Query: 528 GGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAG 587
                MA+ MA GMVPP+ + +ATL+ + KF Q E +AG   +V+G  FI+EGAIPF A 
Sbjct: 444 -----MAATMAAGMVPPIGMGIATLIARRKFAQTEREAGKAALVLGCCFISEGAIPFAAK 498

Query: 588 DPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIAL---TSNPLLYLLYIAVGAVIA 644
           DP R IP+ I G A+TGAL    G KL+APHGG+FV+ +    ++ LLYL+ I  G+++ 
Sbjct: 499 DPLRVIPASIAGGALTGALSMAFGAKLLAPHGGLFVLLIPNAINHALLYLVAILAGSLVT 558

Query: 645 GILFGSLRK 653
           G+++  +++
Sbjct: 559 GVIYAVIKQ 567



 Score = 49.7 bits (117), Expect = 4e-10
 Identities = 28/108 (25%), Positives = 48/108 (44%)

Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228
           L+ VTAC  G+  + +    L+  A  +G    VE +    +G+ LT   I  A  V++ 
Sbjct: 3   LLIVTACPNGMVTSVLTSRLLEAAAHRLGWSTAVEVHDPKAIGSPLTPAQIANADLVVVV 62

Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSD 276
               + + RF GK +     +E +  PE  +    D  +E   AD ++
Sbjct: 63  KTGPLSLQRFVGKRVAQSTPSEALLDPEAFLRSAADTASELQQADEAE 110


Lambda     K      H
   0.320    0.137    0.381 

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: 831
Number of extensions: 41
Number of successful extensions: 9
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: 655
Length of database: 579
Length adjustment: 37
Effective length of query: 618
Effective length of database: 542
Effective search space:   334956
Effective search space used:   334956
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