GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_04042 in Pseudomonas fluorescens FW300-N2E3

Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter

Query= uniprot:A0A2Z5MFR8
         (461 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_05965 AO353_05965 aromatic
           amino acid transporter
          Length = 466

 Score =  634 bits (1634), Expect = 0.0
 Identities = 309/460 (67%), Positives = 370/460 (80%), Gaps = 9/460 (1%)

Query: 2   DNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMI 61
           D  LQQ  LKRGLKNRHIQLIALGGAIGTGLFLGSA VL++AGPSMILGYAI G IAF+I
Sbjct: 3   DEQLQQGVLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLI 62

Query: 62  MRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWW 121
           MRQLGEM+ +EPVAGSFSHFA+ YWG F GFLSGWNYWVLYVLV MAELTAVG YV +WW
Sbjct: 63  MRQLGEMIVEEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWW 122

Query: 122 PGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGP 181
           P VPTWVSA V F  +N IN  NVK +GE EFWFAIIKVVA+IGMI  G Y+LVSG GGP
Sbjct: 123 PEVPTWVSAAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLVSGTGGP 182

Query: 182 QASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVI 241
           QAS+SNLWSHGGFFP+G +GL   +A IMFSFGGLEL+GITAAEA EP+K IPKA+NQV+
Sbjct: 183 QASVSNLWSHGGFFPNGTNGLLMAMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVV 242

Query: 242 YRILIFYICSLAVLLSLYPWNEV---------AAGGSPFVMIFSQIGSTLTANVLNVVVL 292
           YR+LIFY+ +L VLLSLYPW+++         A  GSPFV IF+ IGS   A +LN VVL
Sbjct: 243 YRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQILNFVVL 302

Query: 293 TAALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYL 352
           TAALSVYNSGVY NSRMLYGLAEQG+AP++LMK++++GVP  A+G+SAL T  CV+VNY+
Sbjct: 303 TAALSVYNSGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALITMLCVVVNYV 362

Query: 353 IPAEALGLLMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFM 412
            P EAL LL ALVVA+L++NWA+ISLTHLK R+AM   G    FK+FW P +N++CLAFM
Sbjct: 363 APNEALELLFALVVASLMINWAMISLTHLKFRKAMGQRGIVPGFKAFWSPYTNYLCLAFM 422

Query: 413 ALILVILAMTPGLSVSVLLVPLWLVVMWAGYAFKRRRAAA 452
           A+I+ ++ + PG+  SV  +P+W+++++  Y  +  R  A
Sbjct: 423 AMIIYVMLLIPGVRASVYAIPVWVLILFVFYRIRVARTRA 462


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: 660
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: 466
Length adjustment: 33
Effective length of query: 428
Effective length of database: 433
Effective search space:   185324
Effective search space used:   185324
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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