GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Herbaspirillum seropedicae SmR1

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate HSERO_RS14695 HSERO_RS14695 ABC transporter permease

Query= TCDB::Q8DQI0
         (292 letters)



>FitnessBrowser__HerbieS:HSERO_RS14695
          Length = 293

 Score =  228 bits (581), Expect = 1e-64
 Identities = 117/292 (40%), Positives = 188/292 (64%), Gaps = 3/292 (1%)

Query: 3   LMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFF 62
           ++ QQL+N L LGSVYAL ALG+T+V+G++ +IN +HG I+M+G++    L+    +  +
Sbjct: 1   MLEQQLINALSLGSVYALFALGFTLVFGVLGVINLSHGAIFMLGSYAALLLVEQMALPLW 60

Query: 63  VALIVAMLATAILGVVIEFLAYRPLR--HSTRIAVLITAIGVSFLLEYGMVYLVGANTRA 120
           VAL++AM+AT +LG++I+ L  +PLR  ++  +  +I  IGV+ ++      L GA  + 
Sbjct: 61  VALLLAMVATGLLGLIIDVLVLKPLRKRNAPHLIPMIATIGVAIMITNISQGLFGAENKR 120

Query: 121 FPQA-IQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQ 179
           FPQ  I      LG + +T VQ+ I+ I+ +LM++L  +++KT++G+A+RA++    AA 
Sbjct: 121 FPQGTIPEESVSLGNLHITAVQVAIIVIAFVLMVVLLGVMRKTQLGRALRAIAESPKAAY 180

Query: 180 LMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIP 239
           L+GINV      T    +AL GAAGVL+ + +N++ P MG     K     +LGG+G I 
Sbjct: 181 LLGINVEGLFLLTSFAAAALGGAAGVLVGVSFNAISPFMGQPMLHKGIAVIILGGMGDIR 240

Query: 240 GAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKNVKEK 291
           GA +GG  +G  E    A+  SDFRDA+ +G+L LIL+V+P+G+ GK ++ K
Sbjct: 241 GAMIGGLFLGFAEVLTVAYISSDFRDAVAFGLLFLILLVKPSGMFGKVLERK 292


Lambda     K      H
   0.330    0.146    0.407 

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: 247
Number of extensions: 16
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: 292
Length of database: 293
Length adjustment: 26
Effective length of query: 266
Effective length of database: 267
Effective search space:    71022
Effective search space used:    71022
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