GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_04042 in Pseudomonas fluorescens FW300-N1B4

Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate Pf1N1B4_1580 Histidine transport protein (permease)

Query= uniprot:A0A2Z5MFR8
         (461 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580 Histidine transport
           protein (permease)
          Length = 469

 Score =  395 bits (1014), Expect = e-114
 Identities = 194/452 (42%), Positives = 285/452 (63%), Gaps = 5/452 (1%)

Query: 9   GLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEM 68
           GLKRGL  RHI+ +ALG AIGTGLF GSAS +Q AGP+++L Y IGG   FM+MR LGEM
Sbjct: 7   GLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEM 66

Query: 69  VAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWV 128
               PVAGSF  +A  Y G   GF+ GW Y    V+V MA++TA G Y+ +W+P V  W+
Sbjct: 67  AVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVDRWI 126

Query: 129 SALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSG----HGGPQAS 184
             L   + +  +NL NVK +GE EFW +++KV A++ MIL G  +++ G     G     
Sbjct: 127 WVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGAQATD 186

Query: 185 ISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRI 244
           ISNLWSHGGF P+G  GL    AV+MF+FGG+E+IG+TA EA +PQ+ +P+A+N V  RI
Sbjct: 187 ISNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAINAVPLRI 246

Query: 245 LIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVY 304
           L+FY+ ++ VL+S++PW ++ + GSPFV IF  +G +  A +LN+VV++AA+S  NS ++
Sbjct: 247 LLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSAINSDIF 306

Query: 305 ANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMAL 364
              RM+YGLA+QG+AP+   ++ R GVP++ + + + A    V++NYLIP     L+ ++
Sbjct: 307 GAGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLIPENVFLLIASV 366

Query: 365 VVAALVLNWALISLTHLKSRRAMVAAG-ETLVFKSFWFPVSNWICLAFMALILVILAMTP 423
              A V  W +I  T +  RR+M A     L F   ++P +    +AFM  I  +L   P
Sbjct: 367 ATFATVWVWLMILFTQVAMRRSMSAEQVAQLKFPVPFWPYAPMAAIAFMLFIFGVLGYFP 426

Query: 424 GLSVSVLLVPLWLVVMWAGYAFKRRRAAAHVA 455
               ++++  +W+V++   Y    + AA   A
Sbjct: 427 DTQAALIVGVVWIVLLVLAYLTWVKPAAGQAA 458


Lambda     K      H
   0.327    0.140    0.440 

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: 572
Number of extensions: 25
Number of successful extensions: 2
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: 461
Length of database: 469
Length adjustment: 33
Effective length of query: 428
Effective length of database: 436
Effective search space:   186608
Effective search space used:   186608
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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