GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Marinobacter adhaerens HP15

Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate GFF4122 HP15_4062 spermidine/putrescine ABC transporter, ATP-binding protein

Query= TCDB::Q00752
         (377 letters)



>FitnessBrowser__Marino:GFF4122
          Length = 373

 Score =  233 bits (593), Expect = 8e-66
 Identities = 139/373 (37%), Positives = 220/373 (58%), Gaps = 40/373 (10%)

Query: 4   LNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELK 63
           L+L+++ K++   +   ++  DL+I + EFI  +GPSGCGK+T LR++AG E   +G + 
Sbjct: 6   LSLSNLSKQFGGKT--VLDGLDLEIYDGEFITLLGPSGCGKTTLLRLMAGFEHPDEGTIT 63

Query: 64  IDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQIL 123
           + GE +   AP++R +  VFQ+YAL+PHMSV+DN+A+GLK+    K+ I +RV EA  ++
Sbjct: 64  LAGENLTHTAPENRPLNTVFQHYALFPHMSVFDNVAYGLKMEKRPKDEIRQRVDEALAMV 123

Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHR 183
            L +F  RKP  LSGGQ+QRVA+ RA+V+  ++ L+DEPLS LD KLR +M+ E+ ++ R
Sbjct: 124 QLQDFARRKPHQLSGGQQQRVAIARAVVKRPRLLLLDEPLSALDYKLRRTMQVELKRLQR 183

Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVA 243
            +G T ++VTHDQ EA++++DR+V++            G V+Q+GTP+E+Y RPAN F A
Sbjct: 184 ELGITFVFVTHDQEEALSMSDRVVVLKD----------GLVQQLGTPREVYERPANLFTA 233

Query: 244 GFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLESKGF---KNKNLIFGIRPEDI 300
            F+G    NFF  T++      +DG       G  + L    F     ++L   +RPEDI
Sbjct: 234 RFVGE--TNFFPGTVES----VQDGSIKVDVFGLKRTLRRPDFPVQAEQSLHVLLRPEDI 287

Query: 301 S----------SSLLVQETYPDATVDA--------EVVVSELLGSETMLY-LKLGQTEFA 341
                      +  +V+  Y  +T+D+        EV+ SE    +   +  +LG+    
Sbjct: 288 RVLEPDDENGVAGKIVERNYKGSTLDSVIHLADGTEVLASEFFDEDDPAFDYRLGEPVKV 347

Query: 342 ARVDARDFHEPGE 354
           + VD  ++  P E
Sbjct: 348 SWVDGWEWLLPEE 360


Lambda     K      H
   0.318    0.135    0.375 

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: 358
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: 377
Length of database: 373
Length adjustment: 30
Effective length of query: 347
Effective length of database: 343
Effective search space:   119021
Effective search space used:   119021
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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