GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Brucella inopinata BO1

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_008509836.1 BIBO1_RS16200 ABC transporter ATP-binding protein

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



>NCBI__GCF_000182725.1:WP_008509836.1
          Length = 333

 Score =  377 bits (967), Expect = e-109
 Identities = 196/331 (59%), Positives = 242/331 (73%), Gaps = 2/331 (0%)

Query: 1   MGQIKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTI 60
           M +++L  V K+FG  EVI  +D+ I  GEF VFVGPSGCGKSTLLRLIAGLE+ITSGT+
Sbjct: 1   MAELQLRDVRKSFGSFEVIKGVDMDIRPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60

Query: 61  RIDGEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAA 120
            I+G    N  P++RG+AMVFQSYALYPHM+V +N+AF M++A     E K RI  AA  
Sbjct: 61  SINGAVVNNFNPSRRGIAMVFQSYALYPHMTVYENMAFGMQLASKSRQECKARIHAAAEM 120

Query: 121 LNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELH 180
           L LT YL+R P QLSGGQRQRVAIGRAIVR+P  FLFDEPLSNLDAALRV  RLEI+ LH
Sbjct: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIARLH 180

Query: 181 KRLA-TTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKM 239
           + +  TTMIYVTHDQVEAMT+AD+I VL+ G +EQ+G+P+ELY  P ++FVAGFIGSPKM
Sbjct: 181 QSMEDTTMIYVTHDQVEAMTLADRICVLRDGRVEQIGTPLELYEKPNSLFVAGFIGSPKM 240

Query: 240 NLLTGPQAAQHNAATIGIRPEHLSISETEGMWAGTIGVSEHLGSDTFFHVQCDAFDDPLT 299
           N LTGP A    A T+G+R EHL+I    G W+G +  +E LGSDT+ ++     ++PL 
Sbjct: 241 NFLTGPHAEPFGAHTVGLRSEHLAIVPERGHWSGQVVHTEILGSDTYVYIDL-GLEEPLV 299

Query: 300 VRASGELDLGYGERVFLTPDMTHLHRFGSDG 330
           VR SG      GE + ++P   H+HRF   G
Sbjct: 300 VRESGVSARKPGEALSISPTGDHVHRFDEKG 330


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: 339
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: 334
Length of database: 333
Length adjustment: 28
Effective length of query: 306
Effective length of database: 305
Effective search space:    93330
Effective search space used:    93330
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