GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Pseudomonas fluorescens FW300-N2C3

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 AO356_27685 AO356_27685 ABC transporter ATP-binding protein

Query= TCDB::Q9X103
         (369 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27685
          Length = 367

 Score =  340 bits (872), Expect = 4e-98
 Identities = 180/364 (49%), Positives = 251/364 (68%), Gaps = 12/364 (3%)

Query: 3   MAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62
           MA + ++N+ K +E   + +K  +L V D+EFVV +GPSGCGK+T LR+IAGLEE++DG 
Sbjct: 1   MANLKIKNLQKGFEGFSI-IKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVSDGT 59

Query: 63  IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122
           I +DG+ + +V P  RD+AMVFQ YALYPHM+V +NM+F L L   PK E++++V EAA+
Sbjct: 60  IELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVPKAEVEKKVNEAAR 119

Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182
           IL +  +L+RKP+QLSGGQRQRVA+GRAIVRNPK+FLFDEPLSNLDA LRVQMR EL +L
Sbjct: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARL 179

Query: 183 HHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPM 242
           H  LQAT+IYVTHDQVEAMT+ADK+VV+  G I+Q+G+P E+Y+ PAN+FVAGF+G+P M
Sbjct: 180 HKELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKM 239

Query: 243 NFVNARV--VRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALA 300
            F+  +V  +  +G   +  +G ++ +P+   +     +   +  GIRPE +      LA
Sbjct: 240 GFLKGKVTALDSQGCEVLLDAGTRINLPRSGANL---SVGGAVTLGIRPEHL-----NLA 291

Query: 301 PSPENTITGVVDVVEPLGSETILH-VKVGDDLIVASVNPRTQAKEEQKIDLVLDMTRMHA 359
              + T+    DV E LGS+T  H V    + +   V     ++  ++++L LD    H 
Sbjct: 292 QPGDCTLQVTADVSERLGSDTFCHVVTTSGEALTMRVRGDLASRFGEQLNLHLDAEHCHL 351

Query: 360 FDKE 363
           FD E
Sbjct: 352 FDAE 355


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: 360
Number of extensions: 13
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: 369
Length of database: 367
Length adjustment: 30
Effective length of query: 339
Effective length of database: 337
Effective search space:   114243
Effective search space used:   114243
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