GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Rhodobacter viridis JA737

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_110805339.1 C8J30_RS08100 ABC transporter ATP-binding protein

Query= TCDB::Q9X103
         (369 letters)



>NCBI__GCF_003217355.1:WP_110805339.1
          Length = 348

 Score =  245 bits (625), Expect = 1e-69
 Identities = 123/234 (52%), Positives = 167/234 (71%), Gaps = 2/234 (0%)

Query: 22  VKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDGKVVNDVEPKDRDIA 81
           VK+ NL VE  EF+ LLGPSGCGKTT LRM+AG E  T G I I GK V D++P  R+I 
Sbjct: 19  VKDFNLTVEKGEFISLLGPSGCGKTTVLRMVAGFELPTSGAITIAGKEVTDLKPNQRNIG 78

Query: 82  MVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIENLLDRKPRQLSGGQ 141
           MVFQ YAL+P++TV +N+ FGLK++  PK  ID+RV E   ++G+ +L +R P QLSGGQ
Sbjct: 79  MVFQAYALFPNLTVAQNVGFGLKVKGTPKAAIDKRVEEMLSLIGLPDLGNRYPFQLSGGQ 138

Query: 142 RQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQATIIYVTHDQVEAM 201
           +QRVA+ RA+   P V L DEPLS LDAK+RV +R+E++ +   L  T I+VTHDQ EA+
Sbjct: 139 QQRVALARALAPKPSVLLLDEPLSALDAKVRVSLRNEIRAIQRELGITTIFVTHDQEEAL 198

Query: 202 TMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFVNARVVRGEGG 255
           +M+D++VVM +G   Q+GTP +IYN P+  FVA F+G+  +N +N +V+    G
Sbjct: 199 SMSDRVVVMHEGIADQVGTPFDIYNRPSTRFVASFVGT--LNTLNVQVLDAANG 250


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: 281
Number of extensions: 8
Number of successful extensions: 1
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: 348
Length adjustment: 29
Effective length of query: 340
Effective length of database: 319
Effective search space:   108460
Effective search space used:   108460
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 Sep 24 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