GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HP1174 in Shewanella oneidensis MR-1

Align Glucose/galactose porter (characterized)
to candidate 202604 SO3503 glucose/galactose transporter (NCBI ptt file)

Query= TCDB::P0C105
         (412 letters)



>FitnessBrowser__MR1:202604
          Length = 435

 Score =  194 bits (492), Expect = 6e-54
 Identities = 137/433 (31%), Positives = 223/433 (51%), Gaps = 43/433 (9%)

Query: 14  ETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFI 73
           + S QK+    +  +  LFF+ GF T LN  L+P+LK + QLN  Q+ LI F F+ A   
Sbjct: 4   DKSQQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTF 63

Query: 74  VSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQV 133
            +LP+  +++++ YK G+ +G+ V  I   LFIPAA  +V+ALFL A  V+ +G T+LQ 
Sbjct: 64  TALPSAWVIRKVGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQT 123

Query: 134 AANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLIL--------SAATDATVNA 185
           A NPYV  LG  E+AA+R+++    N     +AP+  + LIL        +  T   ++ 
Sbjct: 124 AVNPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDE 183

Query: 186 EADAVRFPYLLLALAFTVLAIIFAILKPPDV-QEDEPA-LSDKKE-GSAWQYRHLVLGAI 242
            A+ +  PYL +A+   +LA+       P++  EDE A  +DK +  +A  + +L LG +
Sbjct: 184 MANGLVLPYLGMAVFIGILALAVKKSPLPELSNEDEVADHTDKSQIKAALSHPNLALGVL 243

Query: 243 GIFVYVGAEV----SVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMR 298
            +FVYV  EV    ++G+F ++   D      S T     + Y  G  ++ R I      
Sbjct: 244 ALFVYVAVEVIAGDTIGTFALSLGIDHYGVMTSYTMVCMVLGYILGILLIPRVISQPT-- 301

Query: 299 YIDDGKALAFNAFVAIILLF--------------ITVATTGHIAMWSVLA----IGLFNS 340
                 AL  +A + ++L                + +   G +A+   L     +GL N+
Sbjct: 302 ------ALMISAILGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGLANA 355

Query: 341 IMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADA--IGIHLAFLMPIIC 398
           I++P ++ LAL G+G  TS GS +L + I GGA  P+  G ++ A  +G    +++ + C
Sbjct: 356 IVWPAVWPLALSGMGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVMLPC 415

Query: 399 YAYIAFYGLIGSK 411
           Y +I FY + G K
Sbjct: 416 YLFILFYAVKGHK 428


Lambda     K      H
   0.328    0.141    0.420 

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: 500
Number of extensions: 35
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: 412
Length of database: 435
Length adjustment: 32
Effective length of query: 380
Effective length of database: 403
Effective search space:   153140
Effective search space used:   153140
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