Alignments for a candidate for PS417_12065 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_12065 in Herbaspirillum seropedicae SmR1

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 HSERO_RS22220 HSERO_RS22220 D-ribose transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>FitnessBrowser__HerbieS:HSERO_RS22220
          Length = 505

 Score =  348 bits (894), Expect = e-100
 Identities = 197/497 (39%), Positives = 291/497 (58%), Gaps = 11/497 (2%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65
           +L    + K + GV AL+D   ++R G V AL G NGAGKST + IL GI Q D GSI L
Sbjct: 12  VLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIHL 71

Query: 66  NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREP-----RRAGCIVDNKAL 120
            G  V+F    +A+  GI  + QE      ++VAENIW+GR+P     RR    +D + +
Sbjct: 72  GGREVRFASAQDAMRGGITAVHQETVMFEELSVAENIWIGRQPLCGTPRR----IDWRRM 127

Query: 121 NRRTRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQ 180
               R L   LE D+   + +  LSVAQ   VEIA+A S   QV+IMDEPT+A+  HE  
Sbjct: 128 EDEARALFARLEVDLPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIG 187

Query: 181 TLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIV 240
            L++ I +L   G  ++++SH+  E+  +AD Y++ RDG F+ SG +ADI    LV  +V
Sbjct: 188 ELYRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMV 247

Query: 241 GQELTRIDHKVGRECAANTC--LQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEF 298
           G+E+ ++  +        T   L+V +LS   EF D+S  +R GEILG YGL+G+GRSE 
Sbjct: 248 GREVGQVFSRAASNTEDQTAPVLEVKHLSHPSEFDDVSFAVRPGEILGFYGLVGAGRSEV 307

Query: 299 LNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALS 358
           ++ ++GL+    G+V + G+ + +  P   I  G++ V EDR+  G +L+  I  NI L 
Sbjct: 308 MHALFGLSPEAQGAVWIDGREVKLCSPAQAIAHGLAYVPEDRQRQGALLSLPIFQNITLP 367

Query: 359 AYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPV 418
               +  +   + R+E  +A  + ++L++K +     VA +SGGNQQKVVLAK L+T+P 
Sbjct: 368 VLPGIGFFLRRHRRREIDIARRLCEQLELKASHFHQHVAQLSGGNQQKVVLAKWLATQPR 427

Query: 419 CLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVT 478
            L+ DEPT+GID G+K  ++  + + V  G A I+VSSE PE++ +SDRI V   GR+  
Sbjct: 428 VLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVILVSSELPEVMGMSDRIVVMHQGRVQQ 487

Query: 479 ISTDTALSQEALLRLAS 495
           + +    S EAL   AS
Sbjct: 488 VFSRAEASAEALAAAAS 504



 Score = 65.1 bits (157), Expect = 6e-15
 Identities = 54/226 (23%), Positives = 101/226 (44%), Gaps = 11/226 (4%)

Query: 24  DGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAAGI 83
           D   ++R G +    G  GAG+S  +  L G++    G++ ++G  V+   P++A+A G+
Sbjct: 283 DVSFAVRPGEILGFYGLVGAGRSEVMHALFGLSPEAQGAVWIDGREVKLCSPAQAIAHGL 342

Query: 84  AMITQELE---PIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRELLDSLEFDVDATSP 140
           A + ++ +    +  + + +NI L   P   G     +   RR  ++   L   ++  + 
Sbjct: 343 AYVPEDRQRQGALLSLPIFQNITL---PVLPGIGFFLRRHRRREIDIARRLCEQLELKAS 399

Query: 141 MHRLSVAQI-----QLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAG 195
                VAQ+     Q V +AK  +   +V+I+DEPT  I       + + I  L AQG  
Sbjct: 400 HFHQHVAQLSGGNQQKVVLAKWLATQPRVLILDEPTKGIDIGSKAAVHRFIGELVAQGLA 459

Query: 196 IVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVG 241
           ++ VS  L E+  ++D   +   G   +    A+   + L     G
Sbjct: 460 VILVSSELPEVMGMSDRIVVMHQGRVQQVFSRAEASAEALAAAASG 505


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: 588
Number of extensions: 27
Number of successful extensions: 6
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: 495
Length of database: 505
Length adjustment: 34
Effective length of query: 461
Effective length of database: 471
Effective search space:   217131
Effective search space used:   217131
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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Steps (tab-delimited)
Rules (tab-delimited)
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
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