GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alsT in Escherichia coli BW25113

Align Amino-acid carrier protein, AlsT (characterized)
to candidate 14152 b0007 predicted transporter (NCBI)

Query= TCDB::Q45068
         (465 letters)



>FitnessBrowser__Keio:14152
          Length = 476

 Score =  372 bits (954), Expect = e-107
 Identities = 206/480 (42%), Positives = 289/480 (60%), Gaps = 27/480 (5%)

Query: 3   SFFNSLINIPSDFIW-KYLFYILIGLGLFFTIRFGFIQFRYFIEMFRIVGEKPEGNKG-V 60
           SF NS++       W   + Y+L G G +FT R GF+QFRY  +  + +        G +
Sbjct: 6   SFINSVL-------WGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNSIHPQPGGL 58

Query: 61  SSMQAFFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKV 120
           +S Q+   S A+RVG+GNL GVALAI  GGPGAVFWMWV A +GMA+SF E +LAQLYK 
Sbjct: 59  TSFQSLCTSLAARVGSGNLAGVALAITAGGPGAVFWMWVAAFIGMATSFAECSLAQLYKE 118

Query: 121 RD-GEDFRGGPAYYIQKGLGARWLGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNK 179
           RD    FRGGPA+Y+ +GLG RW+G++FA+ + +++G+IF+ VQ N +A AL  +F    
Sbjct: 119 RDVNGQFRGGPAWYMARGLGMRWMGVLFAVFLLIAYGIIFSGVQANAVARALSFSFDFPP 178

Query: 180 IVVAIVLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIV 239
           +V  I+LAV T   I  GL  V  + Q  VP+MA I++L +L + + NI   P VI +I 
Sbjct: 179 LVTGIILAVFTLLAITRGLHGVARLMQGFVPLMAIIWVLTSLVICVMNIGQLPHVIWSIF 238

Query: 240 KNALGFEQVVGGGIG----GIIVIGAQRGLFSNEAGMGSAPNAAATA--HVSHPAKQGFI 293
           ++A G+++  GG  G      I  G QR +FSNEAGMGS PNAAA A     HPA QG +
Sbjct: 239 ESAFGWQEAAGGAAGYTLSQAITNGFQRSMFSNEAGMGSTPNAAAAAASWPPHPAAQGIV 298

Query: 294 QTLGVFFDTFIICTSTAFIILLY---SVTPKGDGIQVTQAALNHHIGGWAPTFIAVAMFL 350
           Q +G+F DT +ICT++A +ILL    +     +GIQ+ Q A+   +G W   F+ + + L
Sbjct: 299 QMIGIFIDTLVICTASAMLILLAGNGTTYMPLEGIQLIQKAMRVLMGSWGAEFVTLVVIL 358

Query: 351 FAFSSVVGNYYYGETNIEFIKTSK---TWLNIYRIAVIAMVVYGSLSGFQIVWDMADLFM 407
           FAFSS+V NY Y E N+ F++ +     W    RI   A V+ G+L    ++W +AD+ M
Sbjct: 359 FAFSSIVANYIYAENNLFFLRLNNPKAIW--CLRICTFATVIGGTLLSLPLMWQLADIIM 416

Query: 408 GIMALINLIVIALLSNVAYKVYKDYAKQRKQGLDPVFKAKNIPGL---KNAETWEDEKQE 464
             MA+ NL  I LLS V + +  DY +QRK G+ PVF     P +    + + W+D  QE
Sbjct: 417 ACMAITNLTAILLLSPVVHTIASDYLRQRKLGVRPVFDPLRYPDIGRQLSPDAWDDVSQE 476


Lambda     K      H
   0.327    0.142    0.426 

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: 539
Number of extensions: 24
Number of successful extensions: 8
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: 465
Length of database: 476
Length adjustment: 33
Effective length of query: 432
Effective length of database: 443
Effective search space:   191376
Effective search space used:   191376
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