GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580
          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 (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