GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztB in Synechococcus elongatus PCC 7942

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine

Query= CharProtDB::CH_011913
         (426 letters)



>FitnessBrowser__SynE:Synpcc7942_0247
          Length = 377

 Score =  211 bits (536), Expect = 4e-59
 Identities = 143/389 (36%), Positives = 207/389 (53%), Gaps = 48/389 (12%)

Query: 29  QIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYSNDDTHFRAL 88
           Q++VLL+   G +WL++N   NL  +G   +F +L   AG+++ ++ I Y   D++ RAL
Sbjct: 23  QLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYRTADSYARAL 82

Query: 89  IEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPLLLWILLMG 148
           + GL+N+L V  +G IL T++GT+ GV   S+NWL+ ++   YV   RN PLLL +++  
Sbjct: 83  VVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVWY 142

Query: 149 TILAETRPVPKDFRLTEAMKAAGEEPKASMW-FFDSVAVTNRGTNLPAPAFDHSLGVVDL 207
             +  + P             A ++P    W +  S+ ++ +G  LP P           
Sbjct: 143 FPILLSLP-------------AAQQP----WHWLGSLYLSKQGIYLPWPQTP-------- 177

Query: 208 GWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSLLILFAPISALL 267
           GW        + ILA+    F  W            A   R    W  L    A ++ L+
Sbjct: 178 GW-------LVVILAIALVLFVSWL-----------AQRQRSPRDWRWLYGAIAVVTVLM 219

Query: 268 YGLGFHLDYPQ-ITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQTE 326
             L   L +PQ +      GG ++   FTALL+ L  YT AFI EI+R GI ++  GQ E
Sbjct: 220 --LLTQLSWPQQLQPGQIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWE 277

Query: 327 AAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGITL 386
           AA ALGL   +T+  +++PQALRVIVP L SQ++   KNSSLAIAV Y DL  T    TL
Sbjct: 278 AAAALGLTRSQTLWQIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTL 336

Query: 387 NQTGRELECMLLMMLIYLTISLTISSLMN 415
           NQTGR +E  L++ML YL I+  IS+ MN
Sbjct: 337 NQTGRPVEVFLILMLTYLAINAVISAGMN 365


Lambda     K      H
   0.326    0.139    0.419 

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: 374
Number of extensions: 13
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: 426
Length of database: 377
Length adjustment: 31
Effective length of query: 395
Effective length of database: 346
Effective search space:   136670
Effective search space used:   136670
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: 50 (23.9 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