GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Marinobacter adhaerens HP15

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 GFF4122 HP15_4062 spermidine/putrescine ABC transporter, ATP-binding protein

Query= TCDB::Q9X103
         (369 letters)



>FitnessBrowser__Marino:GFF4122
          Length = 373

 Score =  255 bits (651), Expect = 2e-72
 Identities = 139/337 (41%), Positives = 212/337 (62%), Gaps = 13/337 (3%)

Query: 1   MRMAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITD 60
           M+   + L N++K +  K V +   +L + D EF+ LLGPSGCGKTT LR++AG E   +
Sbjct: 1   MKQTLLSLSNLSKQFGGKTV-LDGLDLEIYDGEFITLLGPSGCGKTTLLRLMAGFEHPDE 59

Query: 61  GKIYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREA 120
           G I + G+ +    P++R +  VFQ+YAL+PHM+V++N+A+GLK+ K PKDEI +RV EA
Sbjct: 60  GTITLAGENLTHTAPENRPLNTVFQHYALFPHMSVFDNVAYGLKMEKRPKDEIRQRVDEA 119

Query: 121 AKILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELK 180
             ++ +++   RKP QLSGGQ+QRVA+ RA+V+ P++ L DEPLS LD KLR  M+ ELK
Sbjct: 120 LAMVQLQDFARRKPHQLSGGQQQRVAIARAVVKRPRLLLLDEPLSALDYKLRRTMQVELK 179

Query: 181 KLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSP 240
           +L   L  T ++VTHDQ EA++M+D++VV+KDG +QQ+GTP E+Y  PAN+F A F+G  
Sbjct: 180 RLQRELGITFVFVTHDQEEALSMSDRVVVLKDGLVQQLGTPREVYERPANLFTARFVGE- 238

Query: 241 PMNFVNARVVR-GEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFAL 299
             NF    V    +G + +   G K  + +          ++ +   +RPEDI      L
Sbjct: 239 -TNFFPGTVESVQDGSIKVDVFGLKRTLRR---PDFPVQAEQSLHVLLRPEDIR----VL 290

Query: 300 APSPENTITGVVDVVEPLGS--ETILHVKVGDDLIVA 334
            P  EN + G +      GS  ++++H+  G +++ +
Sbjct: 291 EPDDENGVAGKIVERNYKGSTLDSVIHLADGTEVLAS 327


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: 369
Number of extensions: 9
Number of successful extensions: 1
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: 373
Length adjustment: 30
Effective length of query: 339
Effective length of database: 343
Effective search space:   116277
Effective search space used:   116277
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