GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16930 in Pseudomonas fluorescens FW300-N2E2

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate Pf6N2E2_162 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:A0A165ZSX8
         (514 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_162 Ribose ABC transport
           system, ATP-binding protein RbsA (TC 3.A.1.2.1)
          Length = 517

 Score =  367 bits (941), Expect = e-106
 Identities = 211/497 (42%), Positives = 301/497 (60%), Gaps = 6/497 (1%)

Query: 19  NGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIGEQT 78
           +GIGK++     L +I+     G+V AL GENGAGKSTL KI+GG   P++G +Q   Q 
Sbjct: 13  SGIGKTY-AQPVLTDINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGQD 71

Query: 79  MAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALTLLKG 138
                   +   GV ++ QEL+L+P ++VAENLFL +LP   G ++R  LR+ A+  +  
Sbjct: 72  YRPGSRTQAEELGVRMVMQELNLLPTLSVAENLFLDNLPNHGGWISRKQLRKAAIEAMAQ 131

Query: 139 LA-DEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRL 197
           +  D IDP   VG L +G +Q+VEIA+ L    HV+  DEPT+ L+ARE++ L   I RL
Sbjct: 132 VGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRL 191

Query: 198 RDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQDIY 257
           +  G  ++Y+SHR+EE+ R+   + V +DG  V   E M+    +QLVT MVGR++ +  
Sbjct: 192 QARGVSIIYISHRLEELARVAQRIAVLRDGNLV-CVEPMANYNSEQLVTLMVGRELGEHI 250

Query: 258 DYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQR 317
           D  PR+ G  AL VKGL        VSF+V  GEI G+ GL+GAGRTELLRL+ G +   
Sbjct: 251 DLGPRQIGAPALTVKGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADTAD 310

Query: 318 EGSLVLHD--KELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTLG 375
            G++ L    + + +RSP DA+A G+ L  EDRK EG++   S+  NI +   P  S+ G
Sbjct: 311 SGTVALGSPAQVVSIRSPADAVAHGIALITEDRKGEGLLLTQSIAANIALGNMPEISSAG 370

Query: 376 CLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPT 435
            L+ GD E   A +Q+ ++++++ +  Q +  LSGGNQQK ++GRWL     V+L DEPT
Sbjct: 371 -LVNGDAELALAQRQVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCAVMLFDEPT 429

Query: 436 RGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQAN 495
           RGID+GAK +IY ++  L   G A++VVSSDL E+M I DRI VL  G +     RD   
Sbjct: 430 RGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWT 489

Query: 496 ESNLLQLALPRQRVADA 512
           + +LL  A    +  DA
Sbjct: 490 QDDLLAAAFAGYQKRDA 506


Lambda     K      H
   0.320    0.138    0.391 

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: 691
Number of extensions: 39
Number of successful extensions: 10
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: 514
Length of database: 517
Length adjustment: 35
Effective length of query: 479
Effective length of database: 482
Effective search space:   230878
Effective search space used:   230878
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