GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Herbaspirillum seropedicae SmR1

Align proline porter II (characterized)
to candidate HSERO_RS00050 HSERO_RS00050 membrane protein

Query= CharProtDB::CH_024324
         (500 letters)



>FitnessBrowser__HerbieS:HSERO_RS00050
          Length = 437

 Score =  263 bits (672), Expect = 9e-75
 Identities = 135/439 (30%), Positives = 239/439 (54%), Gaps = 11/439 (2%)

Query: 24  RKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83
           ++ + AA +GNA+EW+DF VYGF +  + ++FFP  +    ++ ALATF + F +RP+GG
Sbjct: 8   QRQVIAAIVGNALEWYDFIVYGFFSAIIARLFFPADNEYTSLLVALATFGIGFFMRPVGG 67

Query: 84  LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143
           +  G+  D+ GR+  + + IV+M+++   I   P+Y TIGI API++++ +M QGF+ GG
Sbjct: 68  VLLGLYADRKGRKAAMQVIIVLMTLAIAIIAFTPTYATIGIAAPIMIVVARMLQGFATGG 127

Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203
           EY+ ++ F+ E +P  KRG  GSW   G       GAG+  L++  +       WGWR+P
Sbjct: 128 EYSSSTAFLVESAPAHKRGLYGSWQLVGQCLAVFCGAGMGALVTRNLSPEALDSWGWRLP 187

Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLT 263
           F + L +G +GL++R  + ET  F +  +K          +   +   ++     R +L 
Sbjct: 188 FVLGLLIGPVGLWIRRHMHETDDFLESANK---------PNAAPIKLLDVVKTNLRGVLV 238

Query: 264 CIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMGLLSDRFG 323
            +G VI   V +Y++L  MP++ +  L    D   ++ +  +  +  V P  G LSDR G
Sbjct: 239 SMGQVINGTVAFYVVLVNMPTFANKQLGLPLDQAFMVQMIAVALLTAVIPFAGALSDRLG 298

Query: 324 RRPFVLLGSVALFVLAIPAFILIN-SNVIGLIFAGLLMLAVILNCFTGVMASTLPAMFPT 382
           RR  +L  S+A  ++  P F+ ++ +  +  +    ++L +++    G M + L   FPT
Sbjct: 299 RRTVLLYSSLAFLLMVYPLFVWVSAAPSLPRLLVMQVLLCIVIGANFGPMPTALSEQFPT 358

Query: 383 HIRYSALAAAFNI-SVLVAGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLITGVTMKET 441
            +R + LA A+N+ ++L  G  P +  WL ++S + + PA+Y++  A +G+     M++ 
Sbjct: 359 RVRSTGLAVAYNLAAMLFGGFAPFIVTWLTKTSGSPVAPAWYVLFAACIGVSAAWAMRDQ 418

Query: 442 ANRPLKGATPAASDIQEAK 460
           +       T   + I E K
Sbjct: 419 SPAAKNRQTEVFAGIGEIK 437


Lambda     K      H
   0.327    0.142    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: 591
Number of extensions: 35
Number of successful extensions: 4
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: 500
Length of database: 437
Length adjustment: 33
Effective length of query: 467
Effective length of database: 404
Effective search space:   188668
Effective search space used:   188668
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: 51 (24.3 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