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_007681145.1 BN137_RS01325 PTS transporter subunit EIIC

Query= TCDB::P08722
         (625 letters)



>NCBI__GCF_000319285.1:WP_007681145.1
          Length = 622

 Score =  424 bits (1090), Expect = e-123
 Identities = 238/625 (38%), Positives = 362/625 (57%), Gaps = 16/625 (2%)

Query: 3   ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62
           +  R+I+  +GG  NI+SL HC TRLRF L D +K     L+   G++ V  SG QFQV+
Sbjct: 5   QTGRQIIEHLGGEANILSLYHCITRLRFALVDLNKVNRTALENLDGVMGVNLSGDQFQVI 64

Query: 63  IGNHVADVFLAVNS-VAGLDEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGIL 121
           IGN VA +  A+ + +  LD K   +P    + N ++  +  ++GIF+P+I  +A  GIL
Sbjct: 65  IGNEVAPLCQAILAQLPNLDAKKATSPPK--RRNPISVVLEGLAGIFSPIIPAIAGAGIL 122

Query: 122 KGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGAL 181
           KG+L+L L   W    + TY IL S SD +F+F P++L ++AG +FG NP+ A+ +   L
Sbjct: 123 KGVLSLCLALGWVQADNQTYQILMSISDGVFFFMPLVLAFSAGNKFGANPYVAVALAATL 182

Query: 182 VHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPSA 241
            HP +    ++G       + FLG+PV  ++Y+SSVIPI+ +  L S +ER ++ ++P+A
Sbjct: 183 FHPTLTALLKSGGP-----VAFLGVPVASVSYASSVIPILLAVLLLSYVERFIDRFMPAA 237

Query: 242 IKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIFV 301
           +K  F PLL L+++ PVT + +GP   +    ++ G LWL   +   AG ++GG   + +
Sbjct: 238 LKTMFVPLLSLVIVAPVTLIAIGPAGIFFGNTLSGGILWLVANMGWLAGVIVGGTLSLMI 297

Query: 302 MFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAAL 361
           + G+H+ LVP+ INN + LGYD    L   A M Q GAA GVFL  R+ + K +A S + 
Sbjct: 298 ITGMHYVLVPIVINNISKLGYDPFKILFYVANMGQAGAAFGVFLRARNKKLKTLALSTSF 357

Query: 362 TSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQTIPS 421
           ++  GITEPA+YGVN+  K PF  A I GA G         K Y+F L  I      IP+
Sbjct: 358 SAAMGITEPAMYGVNIRFKRPFAAALIGGACGGAFAMALGVKTYAFALSGI----PGIPA 413

Query: 422 TGIDFTVWASVIGGVIAIGCAFVGTVMLHFITAKRQPAQGAPQEKTPEVITP---PEQGG 478
                 +WA +    IA   A + TV+L F    + PAQ A   +    ++P     +  
Sbjct: 414 LVGPTFLWA-MASLAIAFCTAALMTVILGFEEPAQTPAQPAAPPEVVAGVSPVALAREEQ 472

Query: 479 ICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAIGIES 538
           + +P++G + PL  ++D  FA  + GKGIAI+P  GE+ SPV GRI S+F + HA+ + S
Sbjct: 473 LFAPVSGRLTPLASLSDPVFADEIFGKGIAIVPQSGELLSPVNGRIDSVFDSNHALTLIS 532

Query: 539 DDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTTPVLIS 598
           D+G E+LIH+GIDTVKL G+ F+ HV  G  V  G  LISFD+ A++    D +  V+++
Sbjct: 533 DNGAEVLIHIGIDTVKLGGQHFTRHVESGAFVEAGQPLISFDLDALKALNIDPSVIVIVT 592

Query: 599 NSDDFTDVLPHGTAQISAGEPLLSI 623
           N++ + D+ P     ++  E  L +
Sbjct: 593 NTEHYGDISPLKQGDVAPREAFLKL 617


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: 1174
Number of extensions: 73
Number of successful extensions: 4
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: 622
Length adjustment: 37
Effective length of query: 588
Effective length of database: 585
Effective search space:   343980
Effective search space used:   343980
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