GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16925 in Herbaspirillum seropedicae SmR1

Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate HSERO_RS05255 HSERO_RS05255 ribose ABC transporter permease

Query= uniprot:B2SYR4
         (338 letters)



>FitnessBrowser__HerbieS:HSERO_RS05255
          Length = 347

 Score =  181 bits (460), Expect = 2e-50
 Identities = 102/313 (32%), Positives = 183/313 (58%), Gaps = 12/313 (3%)

Query: 31  QQITEYSLIVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDL 90
           Q++  ++ +++ ++ F+  S    +F  ++N++ +  S +  G+++    + + +   DL
Sbjct: 35  QKLLAFASLLLMILFFSFAS---PNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDL 91

Query: 91  SVGSTVAFAGVLCAMVLNATGNTF-IAIVAAVAAGGVIGFVNGAVIAYLRINALITTLAT 149
           SVG+ + F  V+  +VL   G    + I AA+  G + G+++G VIA L++   I TL  
Sbjct: 92  SVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGM 151

Query: 150 MEIVRGLGFIVSHGQAVGVS-SDTFIALGGLSFFG-----VSLPIWVTLLCFIVFG--VM 201
           M +++GL  ++S  + +  + ++ F A+   S  G     + +P  V +L  +  G  ++
Sbjct: 152 MMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASII 211

Query: 202 LNQTVYGRNTLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNA 261
           LN+TV+GR T A+G N EA RL+G+ V+  +V ++   GA+  +AG+I+ASR+ S QP  
Sbjct: 212 LNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPAL 271

Query: 262 AQGFELNVISACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAI 321
            QG+EL+ I+A V+GG SL GG  TI G +IG  IM  + N + +M++   +Q +V G I
Sbjct: 272 GQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVI 331

Query: 322 LLAAVLLDQLKNR 334
           ++ AV LD L+ R
Sbjct: 332 IILAVYLDILRRR 344


Lambda     K      H
   0.326    0.139    0.396 

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: 290
Number of extensions: 20
Number of successful extensions: 3
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: 338
Length of database: 347
Length adjustment: 29
Effective length of query: 309
Effective length of database: 318
Effective search space:    98262
Effective search space used:    98262
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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