GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Alkalihalobacterium alkalinitrilicum DSM 22532

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= TCDB::P54933
         (332 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  210 bits (535), Expect = 4e-59
 Identities = 125/317 (39%), Positives = 178/317 (56%), Gaps = 31/317 (9%)

Query: 1   MGKITLRNVQKRFGEAVV--IPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDG 58
           M  I   NV K +  A    +  L+L+I +GE +  +GPSGCGK+T LR++AG E  + G
Sbjct: 1   MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60

Query: 59  QIMIDGR----DATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRV 114
           +I I       D   +PP KRG+ MVFQ YAL+PH+T++KN+ F L   + + ++ ++R 
Sbjct: 61  KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLN--RWKNRDKKKRA 118

Query: 115 SNAAKILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRL 174
               +++ L  +  R P +LSGGQ+QRVA+ RA+   P   L DEP SNLDA LR  MR 
Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178

Query: 175 EITELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFI 234
           ++T + +    T I VTHDQ +A  ++D++VV+N G I+Q+ +P  +YR PAN FVA F+
Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238

Query: 235 GSPKMNLIEGP--EAAKHGATTIG------------------IRPEHIDLSREAGAWEGE 274
           G  K NLI G      KH  T IG                  IRPE   L+ E G + G 
Sbjct: 239 G--KTNLISGTLCPDLKHVETHIGRVCLPQETDKVIENVMVSIRPEGCRLA-EKGRYAGL 295

Query: 275 VGVSEHLGSDTFLHVHV 291
           V    + G    +HV +
Sbjct: 296 VERVTYSGEYQEVHVRL 312


Lambda     K      H
   0.320    0.137    0.400 

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: 295
Number of extensions: 9
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: 332
Length of database: 351
Length adjustment: 29
Effective length of query: 303
Effective length of database: 322
Effective search space:    97566
Effective search space used:    97566
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 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