GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acaP in Escherichia coli BW25113

Align Aspartate/glutamate permease AcaP (characterized)
to candidate 15023 b0899 putative transport (VIMSS)

Query= SwissProt::A2RL65
         (489 letters)



>FitnessBrowser__Keio:15023
          Length = 476

 Score =  582 bits (1500), Expect = e-170
 Identities = 278/473 (58%), Positives = 363/473 (76%), Gaps = 4/473 (0%)

Query: 4   KKIRWFTVAFIAFNMVWGMGNVVNNFAQQGITVVTSWLLILALYFIPYALIVGQLCSTFK 63
           K++RW+ +A ++F  VWG GNVVNN+A QG+ VV SW+ I ALYF PYALIVGQL STFK
Sbjct: 8   KQLRWYNIALMSFITVWGFGNVVNNYANQGLVVVFSWVFIFALYFTPYALIVGQLGSTFK 67

Query: 64  DSKGGVSSWVENTSTKRLAYYAAWTYWVVHIPYLAQKPQAILIAFGWVGQGNGNLVSQMS 123
           D KGGVS+W+++T    LAY AAWTYWVVHIPYLAQKPQAILIA GW  +G+G+L+ + S
Sbjct: 68  DGKGGVSTWIKHTMGPGLAYLAAWTYWVVHIPYLAQKPQAILIALGWAMKGDGSLIKEYS 127

Query: 124 MTAVALISLAIFLAFLWLSTKGLNTLKVIGGLAGTAMFVMSLLFIVMAIGAPFIAKDFHI 183
           + A+  ++L +F+ F+W++++G+ +LK++G +AG AMFVMSLL++ MA+ AP I  + HI
Sbjct: 128 VVALQGLTLVLFIFFMWVASRGMKSLKIVGSVAGIAMFVMSLLYVAMAVTAPAIT-EVHI 186

Query: 184 ATPDMGNIKTYIPKFDFSYFTTISMLVFAVGGAEKISPYVNQTKNPAKEFPRGMFLLAGM 243
           AT ++   +T+IP  DF+Y TTISMLVFAVGGAEKISPYVNQT+NP KEFP+GM  LA M
Sbjct: 187 ATTNI-TWETFIPHIDFTYITTISMLVFAVGGAEKISPYVNQTRNPGKEFPKGMLCLAVM 245

Query: 244 VGICAVLGSIAMGMIFSSGNLPKDLMANGAYAAFQILGQHFGVGNFLMIVYALTNGVGQI 303
           V +CA+LGS+AMGM+F S N+P DLM NG Y AFQ LG+++ +GN LM++YA+ N +GQ+
Sbjct: 246 VAVCAILGSLAMGMMFDSRNIPDDLMTNGQYYAFQKLGEYYNMGNTLMVIYAIANTLGQV 305

Query: 304 AALAFSIDAPLRILLADADPEYVPAWLRKKTNKGTLKNGYTLTGILVSIIILLPLLGIGD 363
           AAL FSIDAPL++LL DAD +Y+PA L +    GT  NGY LT +LV+I+I+LP LGIGD
Sbjct: 306 AALVFSIDAPLKVLLGDADSKYIPASLCRTNASGTPVNGYFLTLVLVAILIMLPTLGIGD 365

Query: 364 MNELVKWLTNLNSVVMPMRYLWVFFAFIMLNRAVKHFQSEYKFIKQKRLAMIAGAWCFLF 423
           MN L KWL NLNSVVMP+RYLWVF AFI + R  + ++ EY FI+ K LAM  G WCF F
Sbjct: 366 MNNLYKWLLNLNSVVMPLRYLWVFVAFIAVVRLAQKYKPEYVFIRNKPLAMTVGIWCFAF 425

Query: 424 TLIACVLGMVPKLDYAANPSAWWFQLASNILTPIVLILLGMLLPFIARREQRK 476
           T  AC+ G+ PK++  A  + W FQLA N+ TP VL+ LG++ P +AR+   K
Sbjct: 426 TAFACLTGIFPKME--AFTAEWTFQLALNVATPFVLVGLGLIFPLLARKANSK 476


Lambda     K      H
   0.328    0.140    0.438 

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: 774
Number of extensions: 23
Number of successful extensions: 4
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: 489
Length of database: 476
Length adjustment: 34
Effective length of query: 455
Effective length of database: 442
Effective search space:   201110
Effective search space used:   201110
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: 52 (24.6 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