GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Desulfacinum infernum DSM 9756

Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039
         (367 letters)



>NCBI__GCF_900129305.1:WP_073038605.1
          Length = 368

 Score =  332 bits (850), Expect = 1e-95
 Identities = 181/368 (49%), Positives = 247/368 (67%), Gaps = 21/368 (5%)

Query: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60
           MA +K+  + K F+   +++   L V DKEFVV VGPSGCGKST LR+IAGLEEV+ G I
Sbjct: 1   MAEIKLDQVNKRFKKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEI 60

Query: 61  ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARI 120
            + GR +  V P  RD+AMVFQ+YALYPHM+V KNM+F L   GV + E++++V +AA I
Sbjct: 61  SIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEI 120

Query: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLH 180
           L +  +L+R+P QLSGGQRQRVA+GRAIVR+P+ FLFDEPLSNLDA LRVQMR EL +LH
Sbjct: 121 LGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLH 180

Query: 181 KELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMG 240
           + LQ+T++YVTHDQ+EAMT+AD++VV+  GKI QVG PL++Y +PAN FVAGF+G+P M 
Sbjct: 181 ERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMN 240

Query: 241 FLKGKITRVDSQGCEVQLDAGT-RVSLPLGGRHLS------VGSAVTLGIRPEHLELAKP 293
           FL     R+  +  ++ +D  + R+ +P   RH +      V   V  GIRPE ++  +P
Sbjct: 241 FLD---VRLVEEAGDLWVDGESFRLKVP---RHRAPAFRGHVNRPVIFGIRPEDVK-ERP 293

Query: 294 GDC------ALQVTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQ 347
           GD        L+   DV E +GS+      T    A T R+  ++A R  + + L ++  
Sbjct: 294 GDALPEGVEPLRAEVDVREPIGSEVII-TATVGSHAFTARISPNVAVRVHDPIDLAVNMN 352

Query: 348 HCHLFDAD 355
             HLFD +
Sbjct: 353 KMHLFDPE 360


Lambda     K      H
   0.320    0.137    0.389 

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: 370
Number of extensions: 9
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: 367
Length of database: 368
Length adjustment: 30
Effective length of query: 337
Effective length of database: 338
Effective search space:   113906
Effective search space used:   113906
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