GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Sinorhizobium meliloti 1021

Align ABC transporter (characterized, see rationale)
to candidate SM_b20630 SM_b20630 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:A0A166QFW2
         (381 letters)



>FitnessBrowser__Smeli:SM_b20630
          Length = 361

 Score =  364 bits (934), Expect = e-105
 Identities = 186/351 (52%), Positives = 240/351 (68%), Gaps = 7/351 (1%)

Query: 6   LDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGR 65
           L ++ K  GG+ ++  + L I  G+FVVFVGPSGCGKSTLLR+IAGL+ +  G++ I GR
Sbjct: 12  LSDIRKSYGGLEVIHGIDLTIEEGDFVVFVGPSGCGKSTLLRMIAGLEEVSEGEIAIKGR 71

Query: 66  RVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDK 125
            V DL+P ERG+ MVFQSYALYPHMSV +N+ FGLK+A+TD   +  RV + + IL++D 
Sbjct: 72  DVTDLDPSERGIAMVFQSYALYPHMSVSENLGFGLKMARTDPAEIARRVAQVSAILKIDH 131

Query: 126 LLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGS 185
           LL R+P +LSGGQRQRVA+GRA+ R+PD+ LFDEPLSNLDA LRV MR EIARLH  LG+
Sbjct: 132 LLDRRPGQLSGGQRQRVAIGRAIVRKPDVFLFDEPLSNLDAELRVSMRIEIARLHRELGN 191

Query: 186 TMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSAR 245
           TM+YVTHDQ EAMTLAD+IVVL  GR+EQ GSPR++YE PA+ FVAGF+GSPRMNFL A 
Sbjct: 192 TMVYVTHDQTEAMTLADQIVVLRDGRIEQAGSPRDVYEDPANMFVAGFIGSPRMNFLDAE 251

Query: 246 LQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGVV--VTAV 303
            Q  G   + +T +        D  +L  G  L LGIRPEH+++ A  G   +   V   
Sbjct: 252 WQGDGTIRVGETTL----EAAIDGGSLKHGERLLLGIRPEHIAV-AEPGPERIAAQVEFS 306

Query: 304 EYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADG 354
           EYLG   Y++ +    + L+        WQAG+++   +  D    F  DG
Sbjct: 307 EYLGGTRYLYCQLEDGQSLVVEQREGPNWQAGEKLSFAVPDDRRRFFAEDG 357


Lambda     K      H
   0.320    0.137    0.394 

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: 368
Number of extensions: 17
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: 381
Length of database: 361
Length adjustment: 30
Effective length of query: 351
Effective length of database: 331
Effective search space:   116181
Effective search space used:   116181
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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