GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Alkalihalobacterium alkalinitrilicum DSM 22532

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  214 bits (545), Expect = 3e-60
 Identities = 114/255 (44%), Positives = 156/255 (61%), Gaps = 8/255 (3%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           M+ +  +++ K Y     P V   NL+I + E    +GPSGCGKTTTLRM+AG E  T G
Sbjct: 1   MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60

Query: 61  NLYIGDRRVND----VPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRV 116
            + IGD  V D    +PP+ R I MVFQ+YAL+PH+T+ +N+ FGL   K    +  +R 
Sbjct: 61  KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRWK--NRDKKKRA 118

Query: 117 QEAAKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRA 176
           QE  +++ +     R P  LSGGQ+QRVAL RA+   P+V LMDEP SNLDA LR +MR 
Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178

Query: 177 EIRKLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFI 236
           ++  + ++   T I VTHDQ +A  + DR+VVM +G+IQQ   P+ +Y  P N FVA F+
Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238

Query: 237 GSPAMNFIRGEIVQD 251
           G    N I G +  D
Sbjct: 239 GK--TNLISGTLCPD 251


Lambda     K      H
   0.321    0.138    0.395 

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: 312
Number of extensions: 10
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: 384
Length of database: 351
Length adjustment: 30
Effective length of query: 354
Effective length of database: 321
Effective search space:   113634
Effective search space used:   113634
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