GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01115 in Herbaspirillum seropedicae SmR1

Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate HSERO_RS22215 HSERO_RS22215 branched-chain amino acid ABC transporter permease

Query= reanno::Burk376:H281DRAFT_01115
         (357 letters)



>FitnessBrowser__HerbieS:HSERO_RS22215
          Length = 323

 Score =  120 bits (300), Expect = 6e-32
 Identities = 89/307 (28%), Positives = 153/307 (49%), Gaps = 19/307 (6%)

Query: 19  LLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDLSGVG 78
           LL +  +V+++   +    F+   ++ ++        +LAL  ML +++   GIDLS   
Sbjct: 1   LLALLTVVLILLVGVRAPVFLSAQSMDNLLTDSAITIMLALAQMLVILTR--GIDLSVAS 58

Query: 79  LANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNGVVIARLRLTPILCT 138
              LSGM++A+L          P L   +F  + +++GL+ GLLNG +I  L L PI+ T
Sbjct: 59  NLALSGMMSALLAMHF------PALPVGVFILMAVLIGLMLGLLNGWLIGYLELPPIVVT 112

Query: 139 LGTQLLFTGFAVVISNGASVH-----VDYVE-PLSDIGNGTVLQVPIAFCIFLAAVIVLG 192
           LG+  ++ G   V+S GA V       D++  PL+ +G  T L       +   AV+ + 
Sbjct: 113 LGSMSVYRGMVFVLSGGAWVSSRNMPADFIAFPLARLGGLTHL-----VWLGALAVVAIW 167

Query: 193 WLLKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKW 252
           +L + + FG  LY +G +P AA Y GI     L+ TY + G +A LAG +     + A  
Sbjct: 168 FLARHTRFGRDLYAIGNDPAAAAYVGIASRGRLLWTYGLSGAMAGLAGYLWVARYAVAYT 227

Query: 253 DYGNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWG 312
           +    + L  I   V+GGV+ AGG G++      A  L  +++   ++ +S F+     G
Sbjct: 228 EIAYGFELTVIAACVIGGVSIAGGVGQVSGAVLGALFLSVINNALPIMRISPFWQSALTG 287

Query: 313 FLLLLSL 319
            ++L ++
Sbjct: 288 LVILCAV 294


Lambda     K      H
   0.327    0.143    0.429 

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: 308
Number of extensions: 19
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: 357
Length of database: 323
Length adjustment: 28
Effective length of query: 329
Effective length of database: 295
Effective search space:    97055
Effective search space used:    97055
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