GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5403 in Escherichia coli BW25113

Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate 1936976 b3269 predicted amino-acid transporter subunit (NCBI)

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



>FitnessBrowser__Keio:1936976
          Length = 393

 Score =  474 bits (1219), Expect = e-138
 Identities = 237/376 (63%), Positives = 304/376 (80%), Gaps = 2/376 (0%)

Query: 1   VRAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEAD 60
           VRAW+FQ++ VVAV+ +  +LF NT TNL +RGITSGF FL+R AGFGI QHLIDY + D
Sbjct: 19  VRAWLFQILAVVAVVGIVGWLFHNTVTNLNNRGITSGFAFLDRGAGFGIVQHLIDYQQGD 78

Query: 61  SYARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLL 120
           +Y RVF++GLLNTLLV+ + ++ A++LGF IG+ARLS NW++ KL+T+Y+E+FRNIPPLL
Sbjct: 79  TYGRVFIVGLLNTLLVSALCIVFASVLGFFIGLARLSDNWLLRKLSTIYIEIFRNIPPLL 138

Query: 121 QILFWYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIVL 180
           QI FWYFAV  ++PGPR A +  D  F+S+RGL +P+  + +GF  F+++VV+AIV  V 
Sbjct: 139 QIFFWYFAVLRNLPGPRQAVSAFDLAFLSNRGLYIPSPQLGDGFIAFILAVVMAIVLSVG 198

Query: 181 MTRWANKRFEATGEPFHKFW-VGLALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVL 239
           + R+ NK ++       + W +   L + +P L+  LFGA +HW++P L+GFNF GG VL
Sbjct: 199 LFRF-NKTYQIKTGQLRRTWPIAAVLIIGLPLLAQWLFGAALHWDVPALRGFNFRGGMVL 257

Query: 240 IPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRV 299
           IPEL ALTLAL+VYT+AFIAEI+R+GI++V +GQ EAARSLGL N  TLR+VIIPQALRV
Sbjct: 258 IPELAALTLALSVYTSAFIAEIIRAGIQAVPYGQHEAARSLGLPNPVTLRQVIIPQALRV 317

Query: 300 IIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISI 359
           IIPPLTSQYLN+ KNSSLAA IGYP+MVSLFAGTVLNQTGQAIE IA+TMSVYL IS++I
Sbjct: 318 IIPPLTSQYLNIVKNSSLAAAIGYPDMVSLFAGTVLNQTGQAIETIAMTMSVYLIISLTI 377

Query: 360 SLLMNWYNKRIALIER 375
           SLLMN YN+RIA++ER
Sbjct: 378 SLLMNIYNRRIAIVER 393


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: 481
Number of extensions: 15
Number of successful extensions: 1
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: 393
Length adjustment: 30
Effective length of query: 345
Effective length of database: 363
Effective search space:   125235
Effective search space used:   125235
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:

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