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 1937132 b3795 predicted transporter (NCBI)

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



>FitnessBrowser__Keio:1937132
          Length = 461

 Score =  475 bits (1222), Expect = e-138
 Identities = 229/452 (50%), Positives = 327/452 (72%), Gaps = 3/452 (0%)

Query: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77
           L+R L  RHI L+ALG  IGVGLF+G+A  ++ AGP+++L+YII GL +  IMR++GEM 
Sbjct: 8   LQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPSVLLAYIIAGLFVFFIMRSMGEML 67

Query: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137
              PV GSF+ YA  Y+ P  G+LT W+YWF+W+   ++EITA+ VY+  WFP++ +WI 
Sbjct: 68  FLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPEMAQWIP 127

Query: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197
           AL A+  +   NL AV+ +GE EFWFA+IK+ TII M++ G+G+I FGFGN G ++G SN
Sbjct: 128 ALIAVALVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVIGLGVIFFGFGNGGQSIGFSN 187

Query: 198 LWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257
           L  HGGF   G  G L +L +V+ +Y GVE+IG+TAGEAKNPQ T+ +A+G V WRIL+F
Sbjct: 188 LTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGKVLWRILIF 247

Query: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317
           YVGA+FVI++I+PWNEIG+ GSPFV+TF ++GI  AAGIINFVV+TAALS CN G++S G
Sbjct: 248 YVGAIFVIVTIFPWNEIGSNGSPFVLTFAKIGITAAAGIINFVVLTAALSGCNSGMYSCG 307

Query: 318 RMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLV--PEKVFVWVTSIA 375
           RMLY+LA+N Q PA  AK S +GVP   + +SIA LL+G  LNY++  P++VFV+V S +
Sbjct: 308 RMLYALAKNRQLPAAMAKVSRHGVPVAGVAVSIAILLIGSCLNYIIPNPQRVFVYVYSAS 367

Query: 376 TFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPD 435
               +  W +IL++QL+FR++  A+  A+  +R  L+P ++Y+ +AFL+ V+  M +  D
Sbjct: 368 VLPGMVPWFVILISQLRFRRAHKAA-IASHPFRSILFPWANYVTMAFLICVLIGMYFNED 426

Query: 436 TRVALYVGPAFLVLLTVLFYTFKLQPTGDVQR 467
           TR++L+VG  F++ +T ++  F L   G   +
Sbjct: 427 TRMSLFVGIIFMLAVTAIYKVFGLNRHGKAHK 458


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: 718
Number of extensions: 36
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: 473
Length of database: 461
Length adjustment: 33
Effective length of query: 440
Effective length of database: 428
Effective search space:   188320
Effective search space used:   188320
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:

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