GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Herbaspirillum seropedicae SmR1

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate HSERO_RS14695 HSERO_RS14695 ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__HerbieS:HSERO_RS14695
          Length = 293

 Score =  182 bits (462), Expect = 8e-51
 Identities = 106/293 (36%), Positives = 165/293 (56%), Gaps = 13/293 (4%)

Query: 6   QQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLP 65
           QQL+N L+LGS+Y L A+G+T+V+G++G+IN +HG IFMLG +AAL++            
Sbjct: 4   QQLINALSLGSVYALFALGFTLVFGVLGVINLSHGAIFMLGSYAALLLV---------EQ 54

Query: 66  VAVLLLVMLVVAMLMTSLWNWTIERVAYRPL--RGSFRLAPLITAIGMSITLSNFIQVTQ 123
           +A+ L V L++AM+ T L    I+ +  +PL  R +  L P+I  IG++I ++N  Q   
Sbjct: 55  MALPLWVALLLAMVATGLLGLIIDVLVLKPLRKRNAPHLIPMIATIGVAIMITNISQGLF 114

Query: 124 GPRNKPIP--PMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQ 181
           G  NK  P   +       GN+ ++  Q+ IIVI  VL+ +   ++ +T LGRA RA  +
Sbjct: 115 GAENKRFPQGTIPEESVSLGNLHITAVQVAIIVIAFVLMVVLLGVMRKTQLGRALRAIAE 174

Query: 182 DRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVLG 241
             K A LLG+NV+    +T    AAL   AG +  + +   S   G     K     +LG
Sbjct: 175 SPKAAYLLGINVEGLFLLTSFAAAALGGAAGVLVGVSFNAISPFMGQPMLHKGIAVIILG 234

Query: 242 GIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGR 294
           G+G + GA+ GGL +G  E L  AY +  ++D   F +L  +L+ KP+G+ G+
Sbjct: 235 GMGDIRGAMIGGLFLGFAEVLTVAYISSDFRDAVAFGLLFLILLVKPSGMFGK 287


Lambda     K      H
   0.329    0.143    0.421 

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: 292
Number of extensions: 16
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: 300
Length of database: 293
Length adjustment: 26
Effective length of query: 274
Effective length of database: 267
Effective search space:    73158
Effective search space used:    73158
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 (21.8 bits)
S2: 48 (23.1 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