GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bglF in Cronobacter condimenti 1330

Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_007679744.1 BN137_RS02915 PTS beta-glucoside transporter subunit IIABC

Query= TCDB::P08722
         (625 letters)



>NCBI__GCF_000319285.1:WP_007679744.1
          Length = 619

 Score =  691 bits (1783), Expect = 0.0
 Identities = 344/620 (55%), Positives = 455/620 (73%), Gaps = 9/620 (1%)

Query: 4   LARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVVI 63
           LA+ I+A VGG +NI S++HCATRLRF+LKD+ KA A  LK  PG+IMVV SGGQFQVVI
Sbjct: 6   LAQDILARVGGKENISSVIHCATRLRFRLKDDRKADAPGLKAHPGVIMVVVSGGQFQVVI 65

Query: 64  GNHVADVFLAVNSVAGLDEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGILKG 123
           GNHV DV+LAV   AG+ +   QA ++  +GNLL R + ++SGIFTP IG++AA+GILKG
Sbjct: 66  GNHVHDVWLAVRREAGITDDGAQAEDDGPRGNLLARLIDIVSGIFTPFIGVLAASGILKG 125

Query: 124 MLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGALVH 183
           +LALA+  +W    SGTY I F+ASDALF+FFP++LGYTAGK+FGGNPF  M IGGAL H
Sbjct: 126 LLALAVVCRWIDPASGTYKIWFAASDALFFFFPLVLGYTAGKKFGGNPFITMTIGGALTH 185

Query: 184 PLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPSAIK 243
           P++++AFE  Q+A AL   FLG+PV   NYSSSVIPII +AW+   LE++ N  LP A+K
Sbjct: 186 PVMISAFEASQQAGALADSFLGVPVIWFNYSSSVIPIILAAWVSCWLEKQGNRLLPCAMK 245

Query: 244 NFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIFVMF 303
           NFFTPLLCL V  P+TFL++GP++TW+S+++A GY ++Y   P  AGA  G  WQ+ V+F
Sbjct: 246 NFFTPLLCLGVTVPLTFLVIGPVATWLSQMLANGYQFIYTFAPWLAGAATGALWQVCVIF 305

Query: 304 GLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAALTS 363
           GLHWGLVPL +NN  VLG+D+++P+L+PA+M QVGAAL VFL  RDA++K++AGS+    
Sbjct: 306 GLHWGLVPLMVNNIAVLGHDSLLPMLLPAVMGQVGAALAVFLRSRDARQKMLAGSSVTAG 365

Query: 364 LFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQTIPSTG 423
           +FGITEPAVYGVNLP + PF+  C +GA+G  I+G + T+VYSFG  +IFT  Q IP  G
Sbjct: 366 IFGITEPAVYGVNLPLRRPFIFGCAAGAVGGAIVGLSSTQVYSFGFANIFTIAQMIPPDG 425

Query: 424 IDFTVWASVIGGVIAIGCAFVGTVMLHFITAKRQPAQGAPQEKTPEVITPPEQGGICSPM 483
           ++ T+W  + G + A+  A  G  ++  + A      GA +  T     P  Q    +P+
Sbjct: 426 VNATLWGGLFGTLSALVLA-CGLTLIAGLPA------GAKEANTGSQNVP--QNAALAPL 476

Query: 484 TGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAIGIESDDGVE 543
           +G ++ L +V D TFASGLLG+G AI+PS  +VR+P AG +ASLF T HAIG+  D+G+E
Sbjct: 477 SGTVLALDNVPDPTFASGLLGQGAAIIPSDNQVRAPFAGVVASLFETRHAIGLAGDNGME 536

Query: 544 ILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTTPVLISNSDDF 603
           +LIHVGIDTVKL+G+ F+AHV VGD+VN GD LI FD  AI +AG+DLTTP++ISNSD +
Sbjct: 537 LLIHVGIDTVKLEGQLFTAHVRVGDRVNPGDLLIEFDRQAIIDAGYDLTTPIIISNSDSY 596

Query: 604 TDVLPHGTAQISAGEPLLSI 623
             V       +SAG PLL++
Sbjct: 597 GAVTTVAATAVSAGMPLLTV 616


Lambda     K      H
   0.324    0.141    0.427 

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: 1330
Number of extensions: 81
Number of successful extensions: 2
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: 625
Length of database: 619
Length adjustment: 37
Effective length of query: 588
Effective length of database: 582
Effective search space:   342216
Effective search space used:   342216
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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