GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__MR1:202604 SO3503 glucose/galactose transporter
           (NCBI ptt file)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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