GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Herbaspirillum seropedicae SmR1

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate HSERO_RS00890 HSERO_RS00890 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__HerbieS:HSERO_RS00890
          Length = 404

 Score =  254 bits (650), Expect = 3e-72
 Identities = 155/366 (42%), Positives = 214/366 (58%), Gaps = 48/366 (13%)

Query: 113 IALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAV 172
           + LLL  M+V      Q   ++V    + +L Y+MLA GLN+VVG AGLLDLGY+AFYA+
Sbjct: 19  LLLLLALMIVFPFVAQQFGNSWVRIMDVALL-YIMLALGLNVVVGFAGLLDLGYIAFYAI 77

Query: 173 GAYSYALLSS--------------------------------YFGLSFWVLLPLSGIFAA 200
           GAYS  LL+S                                   LS W+++P+S   AA
Sbjct: 78  GAYSAGLLASPQFAAVIESFVNTYPSVGNFLVWLCGPEIVQNGIHLSLWLIVPISAFLAA 137

Query: 201 LWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINW---TDVTKGTFGISSIPKATLFGI 257
           L+G +LG P L+LRGDYLAIVTL FGEIIR+ + N     ++T G  GI+ I    +FG+
Sbjct: 138 LFGALLGAPTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNITNGPQGINLIDPIKVFGV 197

Query: 258 PF--DATAGGFAKLF--HLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEAL 313
               +  +G   K+F   +P  +AYY     +L L LC+   + ++RL+   +GRAW A+
Sbjct: 198 SLAGEPGSGSMVKVFGMSMPSVNAYY-----FLFLLLCIGVIFFSVRLQDSRLGRAWVAI 252

Query: 314 REDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIV 373
           REDEIA +++GINT   KL AFA GA F G AG+ F A QGFVSPESF   ES  +LA+V
Sbjct: 253 REDEIAAKAMGINTRNVKLLAFAMGASFGGVAGAMFGAFQGFVSPESFSLTESIAVLAMV 312

Query: 374 VLGGMGSLTGIAIAAIVMVGGTELLREM--SFLKLIFGPDF-TPELYRMLIFGLAMVVVM 430
           VLGG+G + G+ +  +++    E+LR +       IFG  +   E+ R L++GLAMVV+M
Sbjct: 313 VLGGIGHIPGVVLGGVILAALPEVLRHVVEPVQMAIFGKVWIDAEVLRQLLYGLAMVVIM 372

Query: 431 LFKPRG 436
           L +P G
Sbjct: 373 LTRPAG 378


Lambda     K      H
   0.330    0.145    0.432 

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: 583
Number of extensions: 37
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 463
Length of database: 404
Length adjustment: 32
Effective length of query: 431
Effective length of database: 372
Effective search space:   160332
Effective search space used:   160332
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: 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