Alignments for a candidate for rbsA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Herbaspirillum seropedicae SmR1

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate HSERO_RS22465 HSERO_RS22465 sugar ABC transporter

Query= TCDB::Q9X051
         (523 letters)



>FitnessBrowser__HerbieS:HSERO_RS22465
          Length = 518

 Score =  424 bits (1089), Expect = e-123
 Identities = 230/516 (44%), Positives = 336/516 (65%), Gaps = 13/516 (2%)

Query: 10  EVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPD--YEG 67
           E LLE + I K+F GV A+N + ++I  GE   L GENGAGKSTLMKIL+GVYP   +EG
Sbjct: 3   EYLLEMKGIVKSFGGVRALNGIDIKIRPGECVGLCGENGAGKSTLMKILSGVYPHGTWEG 62

Query: 68  QIFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMF 127
           +I  +GK ++  + R+ +  GI +I QEL LVP LS AENIF+  E     G + Y  M+
Sbjct: 63  EILWDGKPLQAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHEITLPGGRMNYPAMY 122

Query: 128 EQASKLFSKLGV-NIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETE 186
            +A +L  +L + +I+    V       QQ+V IAKAL+ DA+++I+DEP+S++   E  
Sbjct: 123 RRAEELMRELNMPDINVALPVSQYGGGHQQLVEIAKALNKDARLLILDEPSSSLTASEIG 182

Query: 187 QLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMV 246
            L  II+ LK  G + +YISH+L+E+ E+ D + V+RDG+ +   P++E D DK++  MV
Sbjct: 183 VLLKIIKDLKARGVACVYISHKLDEVAEVCDTISVIRDGKHIATTPMQEMDVDKIITQMV 242

Query: 247 GRSIDQFFIKERATITDEIFRVEGIKLWSLDR-KKLLVDDVSFYVRKGEVLGIYGLVGAG 305
           GR I   + +    I + +     I  + +D  ++  VDDVSF VR+GE+LGI GLVGAG
Sbjct: 243 GREITAMYPERNHAIGEVVLEARNITCYDIDNPRRKRVDDVSFSVRRGEILGIAGLVGAG 302

Query: 306 RTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLH 365
           RTEL+ AIFGA+ GR EG+V + GK     SP  +++ G+ +VPEDRK  G++  + V  
Sbjct: 303 RTELVSAIFGAYRGRYEGQVLLEGKPADTSSPLKSIRRGLCMVPEDRKHHGIVPDLDVGQ 362

Query: 366 NITLPSVVMKLIVRKFGL---IDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKV 422
           NITL       ++ +F     ID   E + ++  I ++ +KT +P+  + +LSGGNQQK 
Sbjct: 363 NITLT------VLNRFSRGSRIDGSAELKTIQDEIGRMRVKTATPFLPITSLSGGNQQKA 416

Query: 423 VLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDR 482
           VLAK L  +PKVL+LDEPTRG+DV AK+EIY+LISE+A +G+ ++MVSSEL E+L +SDR
Sbjct: 417 VLAKMLLAQPKVLILDEPTRGVDVGAKAEIYRLISELAKAGLAIIMVSSELAEVLGVSDR 476

Query: 483 ILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVKVET 518
           +LV+ EGR   +F+ + +++E +L AAI + V   T
Sbjct: 477 VLVIGEGRLRGDFVNDNLSQETVLAAAINQPVPQAT 512



 Score = 90.5 bits (223), Expect = 1e-22
 Identities = 63/246 (25%), Positives = 122/246 (49%), Gaps = 20/246 (8%)

Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHP-GRTEGKVFIGGKEIKIHSPRDAV 341
           ++ +   +R GE +G+ G  GAG++ L++ + G +P G  EG++   GK ++ HS RD  
Sbjct: 21  LNGIDIKIRPGECVGLCGENGAGKSTLMKILSGVYPHGTWEGEILWDGKPLQAHSVRDTE 80

Query: 342 KNGIGLVPEDRKTAGLILQMSVL------HNITLPSVVMKLIVRKFGLIDSQLEKEIVRS 395
             GI ++ ++     L+ ++SV       H ITLP   M      +  +  + E+ +   
Sbjct: 81  AAGIVIIHQELM---LVPELSVAENIFMGHEITLPGGRMN-----YPAMYRRAEELMREL 132

Query: 396 FIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKL 455
            +  +N+  P     V    GG+QQ V +AK L    ++L+LDEP+  +  +    + K+
Sbjct: 133 NMPDINVALP-----VSQYGGGHQQLVEIAKALNKDARLLILDEPSSSLTASEIGVLLKI 187

Query: 456 ISEMAVSGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVK 515
           I ++   G+  V +S +L E+  + D I V+ +G+  A    +E+  + ++   + R + 
Sbjct: 188 IKDLKARGVACVYISHKLDEVAEVCDTISVIRDGKHIATTPMQEMDVDKIITQMVGREIT 247

Query: 516 VETTQR 521
               +R
Sbjct: 248 AMYPER 253


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: 658
Number of extensions: 31
Number of successful extensions: 11
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: 518
Length adjustment: 35
Effective length of query: 488
Effective length of database: 483
Effective search space:   235704
Effective search space used:   235704
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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