Aligments for a candidate for rbsA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Aligments for a candidate for rbsA in Acidovorax sp. GW101-3H11

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= TCDB::Q9X051
         (523 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_609 L-arabinose
           transport ATP-binding protein AraG (TC 3.A.1.2.2)
          Length = 505

 Score =  394 bits (1011), Expect = e-114
 Identities = 224/512 (43%), Positives = 323/512 (63%), Gaps = 16/512 (3%)

Query: 11  VLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYP--DYEGQ 68
           +LLE RNI KTFPGV+A+N V LQ+  GE+ A+VGENGAGKSTLMK+L+GVYP   Y GQ
Sbjct: 1   MLLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQ 60

Query: 69  IFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFE 128
           I  +G+E  F   R+++  GI +I QEL LVP LS AENIFL  E     GVI++     
Sbjct: 61  ILFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETARH-GVIDWMAAHS 119

Query: 129 QASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQL 188
           +A  L  K+G+   P T V  L   +QQ+V IAKALS   +++I+DEPT+++ + +++ L
Sbjct: 120 RAQALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQAL 179

Query: 189 FNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVG-----EGPIEEFDHDKLVR 243
            +++  LK +G + I ISH+L EI  +AD + V+RDG  V      EGP+ E   D++++
Sbjct: 180 LDLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSE---DRVIQ 236

Query: 244 LMVGRSIDQFFIKERATITDEIFRVEGIKLWSLDRK-KLLVDDVSFYVRKGEVLGIYGLV 302
            MVGR +   + + +  + + +F V   +     R  +  +  +   VR+GE++GI GL+
Sbjct: 237 AMVGREMSDRYPQRQPQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLM 296

Query: 303 GAGRTELLEAIFGAHPG-RTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQM 361
           GAGRTEL  +IFG   G R  G+V + G+ I + +   AV +G+  V EDRK  GL+L  
Sbjct: 297 GAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNE 356

Query: 362 SVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQK 421
            +  N +L ++     V    +IDS  E  + + + EKL I+     Q   NLSGGNQQK
Sbjct: 357 DIQFNTSLANLPG---VSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQK 413

Query: 422 VVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSD 481
           VVL+KWL   P+VL+LDEPTRGIDV AK EIY LI+++A  G  V+++SSE+PE+L ++D
Sbjct: 414 VVLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITD 473

Query: 482 RILVMSEGRKTAEFLREEVTEEDLLKAAIPRS 513
           RI VM+EGR  AE    E ++E +++A +  S
Sbjct: 474 RIYVMNEGRFVAEMPTSEASQEKIMRAIVKAS 505


Lambda     K      H
   0.317    0.137    0.372 

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: 619
Number of extensions: 36
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: 523
Length of database: 505
Length adjustment: 35
Effective length of query: 488
Effective length of database: 470
Effective search space:   229360
Effective search space used:   229360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources