GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Acidovorax sp. GW101-3H11

Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)

Query= reanno::pseudo3_N2E3:AO353_25895
         (367 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2066
          Length = 355

 Score =  301 bits (771), Expect = 2e-86
 Identities = 160/348 (45%), Positives = 227/348 (65%), Gaps = 12/348 (3%)

Query: 7   KNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTIELDGRD 66
           K   KG +   +++ +D+ V   EF++ VGPSGCGKSTLL +IAGL+E T G I + G++
Sbjct: 12  KRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKN 71

Query: 67  ITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARILELGPM 126
           +  + P  RD+AMVFQ+YALYP +SV  N+ FAL++  + K E +K+++E A +L++  +
Sbjct: 72  VVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHL 131

Query: 127 LERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKELQAT 186
           L+R+P QLSGGQRQRVA+GRA+ R P++FLFDEPLSNLDA LRV+MR E+ RLH+    T
Sbjct: 132 LDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGIT 191

Query: 187 MIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLKGKV 246
            +YVTHDQVEAMTL  ++ V+ GG ++Q+G+P E+Y++PAN +VA F+G+P M  L+G V
Sbjct: 192 SVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNLLRGAV 251

Query: 247 TRVERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLNLALPGDCTLQVTADVSE 306
           T  +      +  A   +  P S AN      V LG+RPEH  L +      +    V E
Sbjct: 252 TGGQFG----IQGAALNLAPPPSSAN-----EVLLGVRPEH--LVMQETAPWRGRVSVVE 300

Query: 307 RLGSDTFCHVLTASGEALTMRIRGDLASRYGEQLSLHLDAEHCHLFDA 354
             G DT+  V TA+G ++T+R       + GE + L L   H H FDA
Sbjct: 301 PTGPDTYVMVDTAAG-SVTLRTDAQTRVQPGEHVGLALAPAHAHWFDA 347


Lambda     K      H
   0.321    0.137    0.390 

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: 361
Number of extensions: 20
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 367
Length of database: 355
Length adjustment: 29
Effective length of query: 338
Effective length of database: 326
Effective search space:   110188
Effective search space used:   110188
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 17 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