GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SynE:Synpcc7942_0247 Synpcc7942_0247 ABC-type
           permease for basic amino acids and glutamine
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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