GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Alkalihalobacterium alkalinitrilicum DSM 22532

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF1302
         (334 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  214 bits (546), Expect = 2e-60
 Identities = 130/354 (36%), Positives = 195/354 (55%), Gaps = 36/354 (10%)

Query: 1   MGQIKLESVTK--NFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSG 58
           M  I+ ++VTK  N      +  L+L I +GE    +GPSGCGK+T LR++AG E  T+G
Sbjct: 1   MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60

Query: 59  TIRIDGE----DATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRI 114
            IRI  E    D   +PP KRG+ MVFQ YAL+PH+++ KN+ F +        ++K+R 
Sbjct: 61  KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRW--KNRDKKKRA 118

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

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

Query: 235 GSPKMNLLTG------------------PQAAQH--NAATIGIRPEHLSISETEGMWAGT 274
           G  K NL++G                  PQ          + IRPE   ++E +G +AG 
Sbjct: 239 G--KTNLISGTLCPDLKHVETHIGRVCLPQETDKVIENVMVSIRPEGCRLAE-KGRYAGL 295

Query: 275 IGVSEHLGSDTFFHVQCDA---FDDPLTVRASGELDLGYGERVF--LTPDMTHL 323
           +    + G     HV+  +    +DP+ + A  E D+  G  V   +TP++  L
Sbjct: 296 VERVTYSGEYQEVHVRLQSDQVSNDPMIIYAPIEQDIEIGSVVSFDITPELVAL 349


Lambda     K      H
   0.320    0.138    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: 292
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: 334
Length of database: 351
Length adjustment: 29
Effective length of query: 305
Effective length of database: 322
Effective search space:    98210
Effective search space used:    98210
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