GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Klebsiella michiganensis M5al

Align Amino acid:proton symporter (characterized, see rationale)
to candidate BWI76_RS08460 BWI76_RS08460 dicarboxylate/amino acid:cation symporter

Query= uniprot:A0A0N9WTL5
         (431 letters)



>FitnessBrowser__Koxy:BWI76_RS08460
          Length = 435

 Score =  393 bits (1009), Expect = e-114
 Identities = 215/433 (49%), Positives = 297/433 (68%), Gaps = 8/433 (1%)

Query: 1   MKKNKLPRRIAMGIALGVLVGWACHHFAGSEQSAKEIASYFSMVTDIFLRMIKMIIAPLV 60
           MKK  L + I +G+ LG++ G   ++ A ++ +AK  A   S+ T IFLRM+KMIIAPLV
Sbjct: 1   MKKISLTKMIILGLILGMIAGVIINNMASAD-TAKSYAQDISIFTTIFLRMVKMIIAPLV 59

Query: 61  FATLVGGIASMGNSRSVGRIGARAMAWFVTASVVSLLIGMGLVNLFQPGAGLNMDVAQHA 120
            +TLV GIA MG+++++GRI ++    F+ AS++S+ +G+ +VNLFQPGAG+N  V   A
Sbjct: 60  ISTLVVGIAKMGDAKTLGRIFSKTFFLFICASLLSIALGLVIVNLFQPGAGINF-VPHDA 118

Query: 121 TAAVPVNTGDFSLKAFIGHVFPRSIAEAMANNEILQIVVFSLFFGFALA--GVKRAGYTR 178
            A   V +  F+LK FI H  P SI +AMA NEILQIVVFS+F G +LA  G K     +
Sbjct: 119 GAVAAVQSEPFTLKVFISHAVPTSIVDAMARNEILQIVVFSIFLGCSLAAIGEKAEPIVK 178

Query: 179 ITDSIEELAKVMFKITDYVMAFAPIGVFAAIASAITTQGLGLLVDYGKLIAEFYLGILIL 238
           + DS   L  VM K+T YVM FAP+ VFAAI+  I  +GLG++V  G  + EFYL + +L
Sbjct: 179 VLDS---LVHVMLKLTGYVMLFAPLTVFAAISGLIAERGLGVMVSAGIFMGEFYLTLGML 235

Query: 239 WALLFGAGYLFLGRSVFHLGKLIREPILLAFSTASSESAYPKTIEALEKFGAPKRVSSFV 298
           WA+L G   + +G  +  L K I EP LLAF+T+SSE+A+P T++ LEKFG   +++SFV
Sbjct: 236 WAILIGLSTVIVGPCISRLTKAIFEPALLAFTTSSSEAAFPGTLDKLEKFGVSSKIASFV 295

Query: 299 LPLGYSFNLDGSMMYQAFAILFIAQAYNIDLSFTQQLLILLTLMITSKGMAGVARASVVV 358
           LP+GYSFNL GSM Y +FA +FIAQA N+ LS  +Q+ +LL LM+TSKGMAGV RAS+VV
Sbjct: 296 LPIGYSFNLVGSMAYCSFATVFIAQACNVHLSMGEQITMLLILMLTSKGMAGVPRASMVV 355

Query: 359 VAATLPMFNLPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSESHEEADEEEGEH 418
           +AATL  FN+PEAGL+L++G+D FLDM R+ATNV+ N++  A+V + E     +   G  
Sbjct: 356 IAATLNQFNIPEAGLILLMGVDPFLDMGRSATNVMSNAMGAAIVGRWEGEHYGEGCRGT- 414

Query: 419 APARSRSEPVPVA 431
           AP +   +  P +
Sbjct: 415 APVKKPEQDRPAS 427


Lambda     K      H
   0.325    0.138    0.392 

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: 460
Number of extensions: 20
Number of successful extensions: 5
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: 431
Length of database: 435
Length adjustment: 32
Effective length of query: 399
Effective length of database: 403
Effective search space:   160797
Effective search space used:   160797
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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