GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcC in Shewanella loihica PV-4

Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate 5208227 Shew_0739 aromatic amino acid permease (RefSeq)

Query= SwissProt::P0AAD8
         (443 letters)



>FitnessBrowser__PV4:5208227
          Length = 423

 Score =  344 bits (882), Expect = 4e-99
 Identities = 189/428 (44%), Positives = 259/428 (60%), Gaps = 22/428 (5%)

Query: 13  KQSSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHRALAR 72
           ++  W +SDTTW L LFGTA+GAG+LF PI AG GG  P++LM V+  P+ +  HR L+R
Sbjct: 14  QRQGWTRSDTTWMLSLFGTAVGAGILFLPINAGMGGFWPLVLMAVIIGPMTYLAHRGLSR 73

Query: 73  LCLSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWENQLG 132
              S      +IT  VEE+FG   G  IT LYFFAI P++ IYGV ITNT  +F  NQLG
Sbjct: 74  FVCSSQRQGSDITHVVEEYFGVGAGKAITLLYFFAIYPIVLIYGVGITNTVDSFIVNQLG 133

Query: 133 FAPLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNSAVID 192
            A   R  ++  L+L M  V+  G+  M+KV   LV+P +  L  +SL LIP W    + 
Sbjct: 134 MASPPRFLLSGILVLGMMSVMVSGEKFMLKVTQLLVYPLVGILAFMSLYLIPSWKMDALM 193

Query: 193 QVDLGSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRDFTERKC 252
           +V             L TVWL I ++VF+FN SP +S F VS +++Y  +       +K 
Sbjct: 194 EVPAAG-------EFLGTVWLTIPVLVFAFNHSPAISQFSVSLKKQYGSN-----AAKKA 241

Query: 253 SQIISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGTKTTFA 312
             I+   SM++V  VM F FSC+ +LSPA +AEAKAQN+P+LSYLAN  AS         
Sbjct: 242 DVILRNTSMMLVGFVMLFVFSCVLSLSPAQLAEAKAQNLPILSYLANVHASG-------- 293

Query: 313 ITLEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLGKLNTISMIFIM 372
             + Y   IIA++AI  SFFGHYLG  EGL G++ K   +    +VS  K++   + F+ 
Sbjct: 294 -FVSYFGPIIAVIAIVSSFFGHYLGATEGLKGIITK-QLRSSNKEVSDAKIDKFILGFMF 351

Query: 373 GSTWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFVTVIGL 432
            + W VA  NP+IL +IEA+G PIIA++L L+PMYA+ K P+L  YRGR+ N+ V + GL
Sbjct: 352 LTIWGVAVINPSILGMIEALGGPIIAAILYLMPMYAVYKVPALKAYRGRISNILVILAGL 411

Query: 433 LTILNIVY 440
           L +  I++
Sbjct: 412 LAMTAILF 419


Lambda     K      H
   0.328    0.141    0.430 

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: 541
Number of extensions: 25
Number of successful extensions: 6
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: 443
Length of database: 423
Length adjustment: 32
Effective length of query: 411
Effective length of database: 391
Effective search space:   160701
Effective search space used:   160701
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