GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Phaeacidiphilus oryzae TH49

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_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q9X103
         (369 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  313 bits (803), Expect = 4e-90
 Identities = 179/371 (48%), Positives = 236/371 (63%), Gaps = 9/371 (2%)

Query: 3   MAQVVLENVTKVYEN-KVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDG 61
           MA V  +  T++Y      AV   +L + D EF+VL+GPSGCGK+T+LRM+AGLE++ +G
Sbjct: 1   MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60

Query: 62  KIYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAA 121
            I I  + V  + PKDRDIAMVFQNYALYPHMTV +NM F LK+    K EI  +V EAA
Sbjct: 61  AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120

Query: 122 KILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKK 181
           KIL +   LDRKP+ LSGGQRQRVA+GRAIVR P+VFL DEPLSNLDAKLRV  R+++  
Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180

Query: 182 LHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPP 241
           L  RL  T +YVTHDQVEAMTM D++ V+KDG +QQ+ TP  +Y+ PAN+FVAGFIGSP 
Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPA 240

Query: 242 MNFVNARVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAP 301
           MN V   +   +GG+    S   V+V ++   + AN  DK +  G+RPE +         
Sbjct: 241 MNLVEVPIT--DGGVKFGES--VVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGG 296

Query: 302 SPENTITGVVDVVEPLGSETILH--VKVGDDLI--VASVNPRTQAKEEQKIDLVLDMTRM 357
             +  +   V+VVE LG++  ++   KVG + I  V  V  R    +  ++ +V      
Sbjct: 297 GEDKGLAVTVNVVEELGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAGET 356

Query: 358 HAFDKETEKAI 368
           H F   T K +
Sbjct: 357 HVFSTSTGKRL 367


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: 376
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: 369
Length of database: 369
Length adjustment: 30
Effective length of query: 339
Effective length of database: 339
Effective search space:   114921
Effective search space used:   114921
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