GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TAT1 in Escherichia coli BW25113

Align valine/tyrosine/tryptophan amino-acid permease (characterized)
to candidate 14712 b0576 phenylalanine transporter (NCBI)

Query= CharProtDB::CH_091631
         (619 letters)



>FitnessBrowser__Keio:14712
          Length = 458

 Score =  214 bits (545), Expect = 6e-60
 Identities = 140/436 (32%), Positives = 230/436 (52%), Gaps = 17/436 (3%)

Query: 79  NSELESQEKNNLTKSIKSRHLVMISLGTGIGTGLLVGNGQVLGTAGPAGLVLGYGIASIM 138
           + +  S ++  L + + +RH+ +I+LG  IGTGL +G G  +  AGPA ++LGYG+A I+
Sbjct: 8   SEDTASNQEPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPA-VLLGYGVAGII 66

Query: 139 LYCIIQAAGELGLCYAGLTGNYTRYPSILVDPSLGFAVSVVYTIQWLTVLPLQLVTAAMT 198
            + I++  GE+ +    ++G++  +      P  GF     Y + ++ V   +L  A + 
Sbjct: 67  AFLIMRQLGEM-VVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIY 125

Query: 199 VKYW-TSVNADIFVAVVFVFVIIINLFGSRGYAEAEFIFNSCKILMVIGFVILAIIINCG 257
           ++YW   V   I+ A  F+ +  +NL   R Y E EF F   K+L +IG +   + +   
Sbjct: 126 MQYWFPDVPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLFS 185

Query: 258 GAGDRRYIGAEYWHNPGPFAHGFKGVCTVFCYAAFSYGGIEVLLLSAAEQENPTKSIPNA 317
           G G  +      W   G FA G+ G+        FS+GG+E++ ++AAE  +P KSIP A
Sbjct: 186 GHGGEKASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKA 245

Query: 318 CKKVVYRILLIYMLTTILVCFLVPYNSDELLGSSDSSGSHASPFVIAVASHGVKVVPHFI 377
             +VVYRILL Y+ + +++  L P+   +         S++SPFV+   +    VV   +
Sbjct: 246 VNQVVYRILLFYIGSLVVLLALYPWVEVK---------SNSSPFVMIFHNLDSNVVASAL 296

Query: 378 NAVILISVISVANSSLYSGPRLLLSLAEQGVLPKCLAYVDRNGRPLLCFFVSLVFGCIGF 437
           N VIL++ +SV NS +YS  R+L  L+ QG  PK L  V R G P+    +S     +  
Sbjct: 297 NFVILVASLSVYNSGVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVV 356

Query: 438 VATSDAEEQVFTWLLAISSLSQLFIWMSMSLSHIRFRDAMAKQGRSMNEVGYKAQTGYWG 497
           +      ++ F  L+A+   + L  W+ + L+H+RFR AM +QGR   E  +KA    +G
Sbjct: 357 LINYLLPQKAFGLLMALVVATLLLNWIMICLAHLRFRAAMRRQGR---ETQFKALLYPFG 413

Query: 498 SWL--AVLIAIFFLVC 511
           ++L  A L  I  L+C
Sbjct: 414 NYLCIAFLGMILLLMC 429


Lambda     K      H
   0.324    0.138    0.420 

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: 680
Number of extensions: 30
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: 619
Length of database: 458
Length adjustment: 35
Effective length of query: 584
Effective length of database: 423
Effective search space:   247032
Effective search space used:   247032
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.6 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