GapMind for catabolism of small carbon sources

 

Alignments for a candidate for RR42_RS28305 in Pseudomonas fluorescens FW300-N2C3

Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate AO356_18530 AO356_18530 aromatic amino acid transporter

Query= uniprot:A0A0C4YRF7
         (472 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_18530
          Length = 471

 Score =  394 bits (1011), Expect = e-114
 Identities = 193/454 (42%), Positives = 292/454 (64%), Gaps = 12/454 (2%)

Query: 18  DLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGEL 77
           +L RGLK+RHIQ+IA+GGAIG GLFLG+   +  AGP ++L YAI G   F IMR LGE+
Sbjct: 10  ELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEM 69

Query: 78  LLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWI 137
           ++  PV+GSF+ +A ++ G FAGF +GW+ W ++++ GM+E+TAV  Y+HYW PD+P W+
Sbjct: 70  IVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTWV 129

Query: 138 PALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFS 197
            A A   ++  +N   V VFGE EFWFA+IKVV IV MI +G  ++  G    GP AS +
Sbjct: 130 SAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG--GPQASVT 187

Query: 198 NLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILI 257
           NLW+HGGF P G  G+V+ + I+MF++ G+E++G TA EA  P+ V+P A N V++RILI
Sbjct: 188 NLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRILI 247

Query: 258 FYVGALIIMMALVPWNELKPGV---------SPFVYVFERIGVPGAAAIVNLVVITAAAS 308
           FY+GAL+++++L PW+ L   +         SPFV VF  +G   AA I+N VV+TAA S
Sbjct: 248 FYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFVVLTAALS 307

Query: 309 SCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQV 368
             NSG +   RML  +A+ G AP+A  R+  + VP  +I  SAA+  + VLLNY+VP+  
Sbjct: 308 VYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLNYLVPQHA 367

Query: 369 FVWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVA 428
              + S+ +   +  W++I  +H  +R+ +   + +   F+    PY N++ +AF++ + 
Sbjct: 368 LELLMSLVVATLVINWAMISYSHFKFRQHMNQTQ-QTPLFKALWYPYGNYICLAFVVFIL 426

Query: 429 VLLSLDPGTRVALYVAPVWFALLGIGYRFTKSRA 462
            ++ L PG ++++Y  PVW   + + Y     R+
Sbjct: 427 GVMLLIPGIQISVYAIPVWVVFMWVCYVIKNKRS 460


Lambda     K      H
   0.328    0.142    0.445 

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: 679
Number of extensions: 31
Number of successful extensions: 4
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: 472
Length of database: 471
Length adjustment: 33
Effective length of query: 439
Effective length of database: 438
Effective search space:   192282
Effective search space used:   192282
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