Alignments for a candidate for rbsA in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Echinicola vietnamensis KMM 6221, DSM 17526

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component

Query= TCDB::Q9X051
         (523 letters)



>FitnessBrowser__Cola:Echvi_1282
          Length = 502

 Score =  483 bits (1242), Expect = e-141
 Identities = 259/507 (51%), Positives = 367/507 (72%), Gaps = 14/507 (2%)

Query: 12  LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFL 71
           +L  +NITK F GV A+++V+L++  G V A++GENGAGKSTLMKIL+GVYPDY+G I+ 
Sbjct: 1   MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60

Query: 72  EGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQAS 131
            G  V+F+N R+AQE GI +I QEL+L+P LS  ENIFL REP    G+++  KM ++A+
Sbjct: 61  NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAA 120

Query: 132 KLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNI 191
           +L  +L +N+DP+T V  L   QQQ+V IAKALSL++++IIMDEPTSAI  +E E LF I
Sbjct: 121 QLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGI 180

Query: 192 IRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRSID 251
           IR+L+ EGK++ YISH+L+E+F IADR VV+RDG+ +  G +E    + L++ MVGR I 
Sbjct: 181 IRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREI- 239

Query: 252 QFFIKERATITDEIFR-VEGIKLWSLDRKKL----LVDDVSFYVRKGEVLGIYGLVGAGR 306
              + ER+    +    V  +K  ++   K+    L+ D++F + KGEVLGI+GL+GAGR
Sbjct: 240 ---VIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGR 296

Query: 307 TELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHN 366
           TEL+EA+FG  P     ++ + GK  +   P++A+  G+ LVPEDRK  GL+L M +  N
Sbjct: 297 TELMEALFGVLP-HQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTN 355

Query: 367 ITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAK 426
            +L +VV  ++    GL+D + EK + + ++ +L IK  S  Q+VE LSGGNQQKVVLAK
Sbjct: 356 SSL-TVVDSIL--SGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAK 412

Query: 427 WLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVM 486
           WLA +PKVL+LDEPTRGID+NAK+EIYKLI ++A  G+G+++VSSELPEILA+SDR+LVM
Sbjct: 413 WLATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVM 472

Query: 487 SEGRKTAEF-LREEVTEEDLLKAAIPR 512
           +EGR TA   +  + +E+++L+AAIP+
Sbjct: 473 AEGRLTANIPIDAQTSEDEILQAAIPK 499



 Score =  105 bits (263), Expect = 3e-27
 Identities = 71/240 (29%), Positives = 127/240 (52%), Gaps = 19/240 (7%)

Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVK 342
           +DDVS  ++ G V  I G  GAG++ L++ + G +P   +G ++  G  +K  + RDA +
Sbjct: 17  LDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDY-KGTIYYNGDPVKFQNTRDAQE 75

Query: 343 NGIGLVPEDRKTAGLILQMSVLHNITL---PSVVMKLIVRKFGLID-SQLEKEIVRSFIE 398
            GI ++ ++     LI  +S+  NI L   P   M       GL+D +++ KE  +    
Sbjct: 76  KGINIIHQE---LNLIPYLSIRENIFLGREPETPM-------GLLDVAKMHKEAAQLLHR 125

Query: 399 -KLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLIS 457
            KLN+   +P   V  L  G QQ V +AK L+++ +V+++DEPT  I       ++ +I 
Sbjct: 126 LKLNVDPETP---VSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGIIR 182

Query: 458 EMAVSGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVKVE 517
            +   G  +  +S +L E+ A++DR +V+ +G+       E +TEE L++  + R + +E
Sbjct: 183 ALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREIVIE 242


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: 681
Number of extensions: 18
Number of successful extensions: 8
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: 523
Length of database: 502
Length adjustment: 35
Effective length of query: 488
Effective length of database: 467
Effective search space:   227896
Effective search space used:   227896
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)
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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
the source code
instructions for running GapMind on your computer

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