GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Herbaspirillum seropedicae SmR1

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate HSERO_RS22220 HSERO_RS22220 D-ribose transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__HerbieS:HSERO_RS22220
          Length = 505

 Score =  389 bits (1000), Expect = e-112
 Identities = 213/501 (42%), Positives = 315/501 (62%), Gaps = 10/501 (1%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           +L   GI KRF GVVA+ +V F V   E+++L+GENGAGKSTL+KILTG+ +PD G I +
Sbjct: 12  VLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIHL 71

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
            G  V F S  DA + GI+ +HQE  + + ++VAENI++  + + G  R    R+D   M
Sbjct: 72  GGREVRFASAQDAMRGGITAVHQETVMFEELSVAENIWIGRQPLCGTPR----RIDWRRM 127

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
              ++ L   +       A V++L+ AQR  VEI +AL ++ +++ MDEPT++L+  E  
Sbjct: 128 EDEARALFARLEVDLPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIG 187

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
            L+ II  L+  G +V+F+SH+ DE+  ++DR  V+RDG+ I   +  +     ++ +MV
Sbjct: 188 ELYRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMV 247

Query: 254 GREV-EFFPHGIETRPGEIA--LEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTET 310
           GREV + F         + A  LEV++L    +  +VSF VR GE+LGF GLVGAGR+E 
Sbjct: 248 GREVGQVFSRAASNTEDQTAPVLEVKHLSHPSEFDDVSFAVRPGEILGFYGLVGAGRSEV 307

Query: 311 MLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLP 370
           M  +FG++ +  G ++++GR+V++ +P  AI  G+  +PEDR+ QG +L + +  NI LP
Sbjct: 308 MHALFGLSPEAQGAVWIDGREVKLCSPAQAIAHGLAYVPEDRQRQGALLSLPIFQNITLP 367

Query: 371 SLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNA 430
            L  I  + L    R+E +I+    ++L +K    +Q    LSGGNQQKVVLAKWLAT  
Sbjct: 368 VLPGIGFF-LRRHRRREIDIARRLCEQLELKASHFHQHVAQLSGGNQQKVVLAKWLATQP 426

Query: 431 DILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEIT 490
            +LI DEPT+GID+G+KA +HR I EL AQG AVI++SSELPE++ +SDRIVVM +G + 
Sbjct: 427 RVLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVILVSSELPEVMGMSDRIVVMHQGRVQ 486

Query: 491 AVLDNREKRVTQEEIMYYASG 511
            V    E   + E +   ASG
Sbjct: 487 QVFSRAE--ASAEALAAAASG 505


Lambda     K      H
   0.319    0.138    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: 616
Number of extensions: 30
Number of successful extensions: 8
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: 520
Length of database: 505
Length adjustment: 35
Effective length of query: 485
Effective length of database: 470
Effective search space:   227950
Effective search space used:   227950
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 (21.7 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:

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