GapMind for catabolism of small carbon sources

 

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

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate 202604 SO3503 glucose/galactose transporter (NCBI ptt file)

Query= uniprot:A0A1I2JXG1
         (442 letters)



>FitnessBrowser__MR1:202604
          Length = 435

 Score =  194 bits (492), Expect = 6e-54
 Identities = 139/428 (32%), Positives = 224/428 (52%), Gaps = 29/428 (6%)

Query: 27  MAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLV 86
           + M ++ ++FF+ GF T LN  L+P+LK + +LN  +A L+ F+F+ A    +LP+  ++
Sbjct: 13  LPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWVI 72

Query: 87  ARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALL 146
            ++GYK G+  G+ V  +    F PAA    +  FL A  V+  G T+LQ A N YV  L
Sbjct: 73  RKVGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVNPYVVRL 132

Query: 147 GPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSA--EQIAKLSPAEQVAYRVQE 204
           GPE+SA++R+++   LN     +AP     L+ SA +L +  ++I       Q+    + 
Sbjct: 133 GPEESAAARVSVMGILNKGAGVIAP-----LVFSALILDSFKDRIGTTLTQVQID---EM 184

Query: 205 AQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLV-SPLRHPHVLFGVLA 263
           A  +  PYLG+A+ + +LA+ V    LP L+ + E A     S + + L HP++  GVLA
Sbjct: 185 ANGLVLPYLGMAVFIGILALAVKKSPLPELSNEDEVADHTDKSQIKAALSHPNLALGVLA 244

Query: 264 IFFYVGGEV----AIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLG-AMIGRFIGSALLA 318
           +F YV  EV     IG+F ++ L +   G M+       V  Y LG  +I R I      
Sbjct: 245 LFVYVAVEVIAGDTIGTFALS-LGIDHYGVMTSYTMVCMVLGYILGILLIPRVISQPTAL 303

Query: 319 KLSPRKLLAIFAAI------NMALVLTTMMTKGTVA----MYSVVSIGLFNSIMFPTIFS 368
            +S    L +   I      + A+    ++  G VA    +  +  +GL N+I++P ++ 
Sbjct: 304 MISAILGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGLANAIVWPAVWP 363

Query: 369 LGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLF--ADHIGVQHAFFLPLLCYAYIVFYG 426
           L +  MG +T   S+LLIM I GGA  P   GL   A  +G Q  + + L CY +I+FY 
Sbjct: 364 LALSGMGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVMLPCYLFILFYA 423

Query: 427 LYGSRIKS 434
           + G +++S
Sbjct: 424 VKGHKMRS 431


Lambda     K      H
   0.327    0.140    0.414 

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: 502
Number of extensions: 28
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: 442
Length of database: 435
Length adjustment: 32
Effective length of query: 410
Effective length of database: 403
Effective search space:   165230
Effective search space used:   165230
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