GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Caulobacter crescentus NA1000

Align Glucose/galactose transporter (characterized, see rationale)
to candidate CCNA_01159 CCNA_01159 transporter, major facilitator superfamily

Query= uniprot:A0KXM0
         (423 letters)



>FitnessBrowser__Caulo:CCNA_01159
          Length = 451

 Score =  255 bits (652), Expect = 2e-72
 Identities = 160/432 (37%), Positives = 239/432 (55%), Gaps = 31/432 (7%)

Query: 17  AGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGAYFLVS 76
           A  G  + A+V +T LFF+W  +T L D L+  +K VF+L   +A L  F FF AY ++S
Sbjct: 11  AKGGGVKLAIVYVTCLFFIWALVTNLLDPLLKTMKTVFTLTPVEASLTGFAFFIAYGIMS 70

Query: 77  IPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITILQVAA 136
           +P+   + +LGY + ++ GL     GC +   AA   T+G+FL  LFV ASG+T+LQVAA
Sbjct: 71  LPSAAFLSKLGYARSVMVGLGGIVAGCFIAIAAAKLHTFGVFLVGLFVTASGVTLLQVAA 130

Query: 137 NPYVNALGSSETASSRLNLTQAFNALGTTVAPFFG-SILILSVAASVSSELAQANAEAEV 195
           NP + ++G  E +S RLNL+QAFN+LG     +FG + L+        + +  A  E  +
Sbjct: 131 NPLIASMGKPEESSFRLNLSQAFNSLGAACGLWFGANFLLKGEIFEKDAVITDAMREQAL 190

Query: 196 --VKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTSALQSMHLVLGAV 253
             V   YL +   LA+  ++     + ++R+    AA +    +   +AL S    LGA+
Sbjct: 191 GFVSNVYLAIGLGLALFILL-----IFMVRQKITEAAPKTGQLVNPFTALTSKWANLGAI 245

Query: 254 GIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRFIGSAVMQKIPA 313
           GIF+YVGAEV+I   L+ FL ++HI+ +  EQA     +Y   AM+GRF GSA+++ I  
Sbjct: 246 GIFLYVGAEVAISLHLLLFLEQSHILDISAEQAGKLTTFYMVFAMIGRFAGSALLKTIKD 305

Query: 314 GTVLAFNAFMAALLVLV----------------------AMTTSGSVAMWAILGVGLFNS 351
             +LA  A  A  L LV                      A  T+G +  +A L +GLFNS
Sbjct: 306 YVMLAIVAVGAIALCLVVILTKDMTPSAHAGTVNLLLASAPVTTGLIPAFAALLIGLFNS 365

Query: 352 IMFPTIFSLALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLG-IQLAFILPVVCY 410
           IMFPTIF+L L+     TS  SG+LC+AIVGGA +PL    + +  G + + F  P++CY
Sbjct: 366 IMFPTIFTLTLQRSSAPTSATSGLLCMAIVGGAFLPLAFAKIEEMTGSMAMGFAAPLLCY 425

Query: 411 GFILFYGAKGSK 422
            ++L++     K
Sbjct: 426 VYVLWFALVAKK 437


Lambda     K      H
   0.326    0.138    0.402 

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: 509
Number of extensions: 22
Number of successful extensions: 3
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: 423
Length of database: 451
Length adjustment: 32
Effective length of query: 391
Effective length of database: 419
Effective search space:   163829
Effective search space used:   163829
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