GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Paucidesulfovibrio gracilis DSM 16080

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 WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= TCDB::Q00752
         (377 letters)



>NCBI__GCF_900167125.1:WP_078717009.1
          Length = 370

 Score =  230 bits (586), Expect = 5e-65
 Identities = 134/311 (43%), Positives = 192/311 (61%), Gaps = 24/311 (7%)

Query: 4   LNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELK 63
           + L H+ K++   +   + D  LDI++ EF+  +GPSGCGK+T LR++AG E  + GE+ 
Sbjct: 8   IRLEHVAKEFDGET--VLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEII 65

Query: 64  IDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQIL 123
           +DG  + D  P  R +  VFQ+YAL+PHMSV+DN+AFGL++    K  I +RV +A +++
Sbjct: 66  LDGRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMV 125

Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHR 183
           GL     R+P  LSGGQ+QRVA+ RA+V    V L+DEPLS LD KLRV MR E+ ++ R
Sbjct: 126 GLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRR 185

Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVA 243
            +G T I+VTHDQ EA +++DR+V+M+           G V QVGTP E+Y +P N FVA
Sbjct: 186 EMGITFIFVTHDQEEAFSMSDRVVVMNE----------GCVAQVGTPVEVYEQPVNMFVA 235

Query: 244 GFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLES-KGFKNKNLI-FGIRPEDIS 301
            F+G    N F+         S  G+  A+ EG+   L S +GF+  + I   +RPED  
Sbjct: 236 RFVGE--TNVFEGVAGQ----SDGGILQALVEGRTCELSSHRGFQPGDRIRVLLRPED-- 287

Query: 302 SSLLVQETYPD 312
             LLV+   P+
Sbjct: 288 --LLVEREEPE 296


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: 345
Number of extensions: 15
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: 370
Length adjustment: 30
Effective length of query: 347
Effective length of database: 340
Effective search space:   117980
Effective search space used:   117980
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 Apr 09 2024. 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