GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)

Query= TCDB::Q9X103
         (369 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115
          Length = 381

 Score =  320 bits (821), Expect = 3e-92
 Identities = 172/358 (48%), Positives = 242/358 (67%), Gaps = 12/358 (3%)

Query: 8   LENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDG 67
           L+NV K      + +++ +L +   EFVV +GPSGCGK+T LR+IAGL+ I  G + IDG
Sbjct: 6   LDNVNKQLGGMRI-LRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDG 64

Query: 68  KVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIE 127
           + VND+EP++R + MVFQ+YALYPHM+VY+N++FGLKL K  K  +  RV + A+IL ++
Sbjct: 65  RRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLD 124

Query: 128 NLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQ 187
            LL RKP++LSGGQRQRVA+GRA+ R P + LFDEPLSNLDA LRVQMR+E+ +LH RL 
Sbjct: 125 KLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLG 184

Query: 188 ATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFVNA 247
           +T+IYVTHDQVEAMT+ADKIVV+  G ++Q+G+P E+Y  PA+ FVAGF+GSP MNF++A
Sbjct: 185 STMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSA 244

Query: 248 RV-VRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPSPENT 306
           R+   GE  L          +P +  +  A      +  GIRPE +  K      + + T
Sbjct: 245 RLQTPGETSLVDTLVWGITSLPFDSSNLAAG---TPLSLGIRPEHVSLK------AADGT 295

Query: 307 ITGVVDVVEPLGSETILHVKVG-DDLIVASVNPRTQAKEEQKIDLVLDMTRMHAFDKE 363
              VV  VE LGSET +H++ G D+ ++         +   +++L+LD+  +H FD +
Sbjct: 296 AGVVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDAD 353


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: 363
Number of extensions: 18
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: 381
Length adjustment: 30
Effective length of query: 339
Effective length of database: 351
Effective search space:   118989
Effective search space used:   118989
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: 50 (23.9 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