GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Pseudomonas fluorescens GW456-L13

Align MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate PfGW456L13_1569 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= TCDB::Q9X103
         (369 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1569
          Length = 372

 Score =  244 bits (622), Expect = 4e-69
 Identities = 148/348 (42%), Positives = 203/348 (58%), Gaps = 19/348 (5%)

Query: 6   VVLENVTKVY---ENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62
           V + +V KVY   +   VA+K+ +L + D EF  LLGPSGCGKTT LRMIAG E  T+G+
Sbjct: 12  VSIRSVRKVYGDPKTGPVALKSIDLDIRDNEFFTLLGPSGCGKTTLLRMIAGFEFPTEGE 71

Query: 63  IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKL----RKYPKDEIDRRVR 118
           I + G+ + D  P  R +  VFQ+YAL+PHMT+ EN+AFGL+     +   K ++  RVR
Sbjct: 72  ILLYGENIADRPPFQRPVNTVFQHYALFPHMTIAENLAFGLESHPMGKVLHKTQLAERVR 131

Query: 119 EAAKILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSE 178
           E   ++ +E   +RKP QLSGGQ+QRVA+ RA+  +PKV L DEPLS LD KLR  MR E
Sbjct: 132 EMLALVQMERFANRKPAQLSGGQQQRVALARALAPHPKVLLLDEPLSALDLKLRQAMREE 191

Query: 179 LKKLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIG 238
           LK +  R   T I+VTHDQ EA+TM+D+I V+ +GE+QQ+G P +IY  P N FVA FIG
Sbjct: 192 LKTIQARTGITFIFVTHDQEEALTMSDRIAVLSEGEVQQVGRPEDIYERPRNRFVADFIG 251

Query: 239 SPPMNFVNARVVRGEGGL-WIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLF 297
               NF+   V R E GL W           +   D     +   +   +RPE    +L 
Sbjct: 252 E--TNFIEGTVTRVEDGLAWFAGPAGHPLPAQPCSDV---RVGANVTLSVRPE----RLH 302

Query: 298 ALAPSPENTITGVVDVVEPLGSETILHVKVGDD--LIVASVNPRTQAK 343
            +  + EN +   ++    LG++    V + D   L V + N   Q+K
Sbjct: 303 LVPATTENALPCRIEAQIYLGTDLQYQVSLSDGSRLTVRTPNCVDQSK 350


Lambda     K      H
   0.319    0.138    0.387 

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: 347
Number of extensions: 20
Number of successful extensions: 3
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: 369
Length of database: 372
Length adjustment: 30
Effective length of query: 339
Effective length of database: 342
Effective search space:   115938
Effective search space used:   115938
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