GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_12065 in Pseudomonas fluorescens FW300-N2E3

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_20820 AO353_20820 sugar ABC
           transporter ATP-binding protein
          Length = 517

 Score =  313 bits (802), Expect = 9e-90
 Identities = 197/494 (39%), Positives = 282/494 (57%), Gaps = 10/494 (2%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65
           +L    + K YA  P L    L+L  G V AL G NGAGKST   I+ G+     G +  
Sbjct: 9   VLSVSGIGKTYAQ-PVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQF 67

Query: 66  NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125
            G   +    ++A   GI M+ QEL  +P ++VAEN++L   P   G I   K L +   
Sbjct: 68  QGRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSNGGWI-SRKQLRKAAI 126

Query: 126 ELLDSLEFD-VDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184
             +  +  D +D  + +  L +   Q+VEIA+    DC V+I+DEPT+ +   E + LF+
Sbjct: 127 AAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFE 186

Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244
            I RL A+G  I+Y+SHRL ELA++A   ++ RDG  V    MA+ + + LV  +VG+EL
Sbjct: 187 QITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVGREL 246

Query: 245 -TRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIY 303
              ID  +G        L V  LSR+ +  D+S ++R GEI GI GL+G+GR+E L  I+
Sbjct: 247 GEHID--LGPRHIGAPALTVKGLSRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIF 304

Query: 304 GLTVADSGSVTLQGKP---MPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAY 360
           G   ADSG+V L G P   + I  P   +  G++L+TEDRK  GL+LT SI +NIAL   
Sbjct: 305 GADAADSGTVAL-GSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGNM 363

Query: 361 KRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCL 420
             +SS  ++N+  E  LA+  +  ++I+++S    V+ +SGGNQQKVV+ + L  E   L
Sbjct: 364 PVISSGGIVNSGDEMALAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERECSVL 423

Query: 421 LCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTIS 480
           L DEPTRGID GAK +IY LL +  R G A +VVSS+  EL+ + DRI V   GRL+   
Sbjct: 424 LFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTF 483

Query: 481 TDTALSQEALLRLA 494
              + +Q+ LL  A
Sbjct: 484 ERDSWTQDDLLAAA 497


Lambda     K      H
   0.319    0.135    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: 606
Number of extensions: 29
Number of successful extensions: 9
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: 495
Length of database: 517
Length adjustment: 34
Effective length of query: 461
Effective length of database: 483
Effective search space:   222663
Effective search space used:   222663
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: 52 (24.6 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