Alignments for a candidate for cycA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for cycA in Escherichia coli BW25113

Align L-alanine and D-alanine permease (characterized)
to candidate 14258 b0112 aromatic amino acid transporter (NCBI)

Query= reanno::pseudo5_N2C3_1:AO356_17670
         (473 letters)



>FitnessBrowser__Keio:14258
          Length = 457

 Score =  395 bits (1016), Expect = e-114
 Identities = 195/444 (43%), Positives = 280/444 (63%), Gaps = 4/444 (0%)

Query: 15  GGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALG 74
           G  LKR L  RHI+L+ALG  IG GLFLGSA  I+ AGP I+L Y I G    +IMR LG
Sbjct: 8   GEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLG 67

Query: 75  EMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPR 134
           EM V  PVAGSFS +A  Y G  AGF +GWNYW L+++  +AE+TAV  Y+  W+P++P 
Sbjct: 68  EMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPT 127

Query: 135 WIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALG 194
           W+ A    V + +INL  VK FGE EFWFA+IK++ ++AM+I G G + F  GN G    
Sbjct: 128 WVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFG-GWLLFS-GNGGPQAT 185

Query: 195 ISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRI 254
           +SNLW  GGF+P+G +G++M + ++MF++ G+E++G+TA EA NP+++IP A   V +RI
Sbjct: 186 VSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRI 245

Query: 255 LLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIF 314
           L+FY+G+L V+LS+ PW  +    SPFV+ F  LG    A  +N VV+TAALS  N  ++
Sbjct: 246 LIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVY 305

Query: 315 STGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSI 374
              RML+ LAQ G AP   A     GVP   +L+S     L VL+NYL PE  F  + ++
Sbjct: 306 CNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMAL 365

Query: 375 ATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFP 434
                +  W MI LA +KFR++    +    ++   LYP+ +++ L F+  V+ +M   P
Sbjct: 366 VVSALVINWAMISLAHMKFRRA-KQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTP 424

Query: 435 DTRVALYVGPAFLVLLTVLFYTFK 458
              +++Y+ P +L++L +  Y FK
Sbjct: 425 GMAISVYLIPVWLIVLGI-GYLFK 447


Lambda     K      H
   0.328    0.142    0.444 

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: 636
Number of extensions: 28
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: 473
Length of database: 457
Length adjustment: 33
Effective length of query: 440
Effective length of database: 424
Effective search space:   186560
Effective search space used:   186560
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: 51 (24.3 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources