GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Keio:1936976 b3269 predicted amino-acid
           transporter subunit (NCBI)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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