GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Phaeobacter inhibens BS107

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate GFF2690 PGA1_c27320 putative sugar ABC transporter, ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Phaeo:GFF2690
          Length = 349

 Score =  319 bits (818), Expect = 6e-92
 Identities = 175/366 (47%), Positives = 228/366 (62%), Gaps = 18/366 (4%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           MA++ L ++ KR+G  V V +F+L   D EF+V +GPSGCGKTTT+RMIAGLE  SEG+I
Sbjct: 1   MAQIELRNISKRWGSFVGVDNFDLTIADKEFLVLLGPSGCGKTTTMRMIAGLESASEGDI 60

Query: 61  YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120
            +    VN++ PKDRD+AMVFQ+YALYP+MNVYEN+ F L++R       D +V+ A+ +
Sbjct: 61  LVDGNRVNELEPKDRDVAMVFQSYALYPNMNVYENIRFPLKVRGVDAKTHDEKVRRASAM 120

Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180
           ++++  L+RKP ELSGGQRQRVA+ RAIVREP VFLMDEPLSNLDAKLRV  RA+I  L 
Sbjct: 121 VELDEFLHRKPAELSGGQRQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTRAQIKNLS 180

Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240
             L VTTIYVTHDQ+EAMTL  R+VVM  G +QQV +P  +YD PAN FVA FIGSP+MN
Sbjct: 181 HELAVTTIYVTHDQIEAMTLADRVVVMNKGVVQQVGSPTEIYDRPANAFVASFIGSPAMN 240

Query: 241 FVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEE 300
            +  G+            G R  A     + L    G  V LG R E        ++ + 
Sbjct: 241 LMEGGLS-----------GGRFTAQHTDIAGLSGQDG-PVTLGFRAED------ASVVDS 282

Query: 301 ENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQRLHAFDLE 360
              +   +  +E LG  T + V + G L+  K D     +  D V +   T   H FD +
Sbjct: 283 GGQINAPIYTMELLGDATMVTVRIGGVLVSVKADKTFRAEIDDMVSIHVPTDHCHLFDTQ 342

Query: 361 TDRTIG 366
           T   +G
Sbjct: 343 TGARLG 348


Lambda     K      H
   0.320    0.139    0.400 

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: 362
Number of extensions: 15
Number of successful extensions: 2
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: 376
Length of database: 349
Length adjustment: 29
Effective length of query: 347
Effective length of database: 320
Effective search space:   111040
Effective search space used:   111040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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:

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