GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TT_C0327 in Marinobacter adhaerens HP15

Align Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate GFF3013 HP15_2957 sugar ABC transporter, permease protein

Query= TCDB::Q72KX3
         (369 letters)



>lcl|FitnessBrowser__Marino:GFF3013 HP15_2957 sugar ABC transporter,
           permease protein
          Length = 308

 Score =  139 bits (351), Expect = 8e-38
 Identities = 103/364 (28%), Positives = 166/364 (45%), Gaps = 83/364 (22%)

Query: 4   RILAFLVLLPSVLAVGVFVYGFIGQNLWVSLTDWGKDPAQALALRPELRFVGLENYRELF 63
           R L  LV+ P+ + +GV +YG++   LW  +  +        +  P   FVG + Y +L 
Sbjct: 24  RWLPKLVVAPTFVLIGVGIYGYM---LWTGVLSFTSS-----SFLPVYDFVGFDQYAKLM 75

Query: 64  TGFVDVRFRQSVVNLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMALSFV 123
               + R+  + +NL  F   F+   L +G++LA+ +D+  R EG  RT++L+PMALS +
Sbjct: 76  A---NDRWLTASINLGIFGGLFVLSCLVIGVILAIFLDQRIRQEGAIRTIYLYPMALSMI 132

Query: 124 VTGTIWRWLLQPQGGVNVLPTLFGLPPLSFPWLATREQVLVFDWNRLPFYTALVVGLVLL 183
           VTGT+W+W+L P  G+  L   +G    SF WL + +  +         YT ++      
Sbjct: 133 VTGTVWKWILNPSLGLEKLMHDWGWTSFSFDWLVSSDMAI---------YTIVMA----- 178

Query: 184 YVAYTAYREGERRRALWGLASAGVLLLWAFAFGQGLRLLPYPEVHGFSLALVGVILAAVW 243
                         A+W  +   + L  A   G    ++    V G SL L+        
Sbjct: 179 --------------AVWQASGFVMALFLAGLRGVDSSIIRAARVDGASLPLI-------- 216

Query: 244 QMSGYTMALYLAGLRGIPVEVLEAARVDGASEWQLFRRVIFPMLAPITLSAMIVLGHIAL 303
                                              + ++I P L P+  SA++VL HIA+
Sbjct: 217 -----------------------------------YWKIILPSLRPVFFSAVMVLAHIAI 241

Query: 304 KIFDLVFAM-AGLDYAPTDVPAIYMYLLAFRGNQFAKGAAIGILLLLLVAVVVVPYLATQ 362
           K FDLV AM AG     TD+PA++MY   F   Q   G+A  +L+L  +  ++VPYL ++
Sbjct: 242 KSFDLVMAMTAGGPGYSTDLPAVFMYAHTFTRGQMGLGSASAMLMLGAILALIVPYLYSE 301

Query: 363 LRKE 366
           LR++
Sbjct: 302 LREK 305


Lambda     K      H
   0.331    0.146    0.458 

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: 346
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 369
Length of database: 308
Length adjustment: 28
Effective length of query: 341
Effective length of database: 280
Effective search space:    95480
Effective search space used:    95480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 49 (23.5 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 preprint 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