GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5403 in Synechococcus elongatus PCC 7942

Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine

Query= reanno::pseudo6_N2E2:Pf6N2E2_5403
         (375 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0247 Synpcc7942_0247 ABC-type
           permease for basic amino acids and glutamine
          Length = 377

 Score =  256 bits (653), Expect = 9e-73
 Identities = 150/369 (40%), Positives = 217/369 (58%), Gaps = 19/369 (5%)

Query: 4   WVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEADSYA 63
           WV+Q++ ++ V     +L DN   NL  RG++  F +L++SAGF I +  I Y  ADSYA
Sbjct: 20  WVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYRTADSYA 79

Query: 64  RVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQIL 123
           R  ++GL+N+L V  IG+IL T++G + GVA  S+NW++ +L+  YV V RN P LLQ++
Sbjct: 80  RALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLI 139

Query: 124 FWYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVIS--VVLAIVAIVLM 181
            WYF + LS+P  +   ++  + ++S +G+ +P        WP      VV+  +A+VL 
Sbjct: 140 VWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLP--------WPQTPGWLVVILAIALVLF 191

Query: 182 TRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVLIP 241
             W  +R  +   P    W    L+  I  ++ L+    + W   +L+     GG  L  
Sbjct: 192 VSWLAQRQRS---PRDWRW----LYGAIAVVTVLMLLTQLSWPQ-QLQPGQIRGGLRLSL 243

Query: 242 ELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVII 301
           E  AL L L  YT AFI EI+R GI SV  GQ EAA +LGL    TL ++++PQALRVI+
Sbjct: 244 EFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIV 303

Query: 302 PPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISL 361
           P L SQY+  AKNSSLA  +GYP++ +  A T LNQTG+ +EV  I M  YLAI+  IS 
Sbjct: 304 PSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEVFLILMLTYLAINAVISA 362

Query: 362 LMNWYNKRI 370
            MN   +R+
Sbjct: 363 GMNGLQQRL 371


Lambda     K      H
   0.328    0.141    0.430 

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: 384
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: 375
Length of database: 377
Length adjustment: 30
Effective length of query: 345
Effective length of database: 347
Effective search space:   119715
Effective search space used:   119715
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 (21.8 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 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