GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Alkalihalobacterium alkalinitrilicum DSM 22532

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 WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= TCDB::Q9X103
         (369 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  219 bits (558), Expect = 9e-62
 Identities = 133/344 (38%), Positives = 192/344 (55%), Gaps = 41/344 (11%)

Query: 3   MAQVVLENVTKVYENKVV-AVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDG 61
           M+ +  +NVTK Y      AV   NL + + E + LLGPSGCGKTTTLRM+AG E+ T G
Sbjct: 1   MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60

Query: 62  KIYIDGKVVND----VEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRV 117
           KI I  +VV D    + P+ R I MVFQ+YAL+PH+T+ +N+ FGL   ++   +  +R 
Sbjct: 61  KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLN--RWKNRDKKKRA 118

Query: 118 REAAKILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRS 177
           +E  +++G+     R P +LSGGQ+QRVA+ RA+   PKV L DEP SNLDA LR +MR 
Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178

Query: 178 ELKKLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFI 237
           ++  +  +  AT I VTHDQ +A  ++D++VVM +G IQQI  P E+Y  PAN FVA F+
Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238

Query: 238 GS---------PPMNFVNARVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIR 288
           G          P +  V   + R             V +P+E +  + N     ++  IR
Sbjct: 239 GKTNLISGTLCPDLKHVETHIGR-------------VCLPQETDKVIEN-----VMVSIR 280

Query: 289 PEDIYDKLFALAPSPENTITGVVDVVEPLGSETILHVKVGDDLI 332
           PE           + +    G+V+ V   G    +HV++  D +
Sbjct: 281 PE-------GCRLAEKGRYAGLVERVTYSGEYQEVHVRLQSDQV 317


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: 307
Number of extensions: 18
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: 369
Length of database: 351
Length adjustment: 29
Effective length of query: 340
Effective length of database: 322
Effective search space:   109480
Effective search space used:   109480
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