GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Synechococcus elongatus PCC 7942

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine

Query= reanno::Smeli:SMc02119
         (397 letters)



>FitnessBrowser__SynE:Synpcc7942_0247
          Length = 377

 Score =  232 bits (591), Expect = 2e-65
 Identities = 136/384 (35%), Positives = 209/384 (54%), Gaps = 14/384 (3%)

Query: 9   PERSRSSGSIINDPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASGYDFVRSRA 68
           P R +  G    D ++    +Q + ++++     W+VDN V NL +  ++  +D++   A
Sbjct: 2   PFRLKLQGPFWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSA 61

Query: 69  GFDVGQSLISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKL 128
           GF++G+S I++ +  +Y RAL+VG +N+L V   G+I  T+IG + G+   S NW++ +L
Sbjct: 62  GFNIGESAIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQL 121

Query: 129 SLAYVEVFRNIPPLLVIFFWYSGVLSILPQARDALALPFDIFLSNRGVAFPRPIAEEGAE 188
           S  YV V RN P LL +  WY  +L  LP A+        ++LS +G+  P P       
Sbjct: 122 SRGYVAVVRNTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQTPGW-- 179

Query: 189 YTLLAFVIAVAASVFFARYARKRQLATGERLPVLWTVLGLIIGLPLVTFLVTGAPITFDI 248
              L  ++A+A  +F +  A++      +R P  W  L   I +  V  L+T       +
Sbjct: 180 ---LVVILAIALVLFVSWLAQR------QRSPRDWRWLYGAIAVVTVLMLLTQLSWPQQL 230

Query: 249 PVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPA 308
                  + GG  +  EF +L L L  YT AFI EI+R GI  V  GQ EAA ALG+  +
Sbjct: 231 QPG---QIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRS 287

Query: 309 LTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILNQTGQSIEIVS 368
            T   +VVPQA+R+I+P L SQY+   KNSSLA+A+GY DL A   T LNQTG+ +E+  
Sbjct: 288 QTLWQIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFL 347

Query: 369 IWLIVYLSLSLATSLFMNWYNARM 392
           I ++ YL+++   S  MN    R+
Sbjct: 348 ILMLTYLAINAVISAGMNGLQQRL 371


Lambda     K      H
   0.327    0.141    0.412 

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: 416
Number of extensions: 15
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: 397
Length of database: 377
Length adjustment: 30
Effective length of query: 367
Effective length of database: 347
Effective search space:   127349
Effective search space used:   127349
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.

Links

Downloads

Related tools

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