GapMind for catabolism of small carbon sources

 

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

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate Ac3H11_102 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_102
          Length = 293

 Score =  137 bits (345), Expect = 3e-37
 Identities = 88/296 (29%), Positives = 156/296 (52%), Gaps = 21/296 (7%)

Query: 10  QLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSY--IAFIAITLLAMMGLDS 67
           Q++NGL++G    L+A+G T+++G++ +IN AHGE Y IG+Y  +A +A  +     L  
Sbjct: 11  QMINGLSIGVAVVLMALGLTIIFGLLDVINMAHGEFYAIGAYLAVALLATGMSFWWALVL 70

Query: 68  VPLMMLAAFAASIIVTSAFGYSIER-VAYRPLRGGNR-LIPLISAIGMSIFLQNAVMLSQ 125
            PL+M           +  G+  ER +  R     +R  + L+   G+++ L++A+ ++ 
Sbjct: 71  TPLLM-----------AVLGFVTERGLIQRVFHSKDRHTLTLLLTFGVAVVLEDALKIAF 119

Query: 126 DSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRA 185
            +    +   + G      + M G+     ++ + +    ++  + L + R+ LG   RA
Sbjct: 120 GANPLRLEAPISG-----ATEMLGLFFPNYRLFVMLFGGALIAAVWLLVFRTSLGAIVRA 174

Query: 186 CAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAA 245
            A D  M+  LG+    + A TF  G ALA +A VLL   Y V  P +G    + AF+  
Sbjct: 175 AAYDRNMSASLGVPVQLVYAGTFAFGVALAGIAGVLLAPIYSVF-PTMGKDFVLIAFSVV 233

Query: 246 VLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGR 301
           ++GG+GSI GA+L GLLL   ++  +      + D + FG+++LVL++RP G+ G+
Sbjct: 234 IIGGMGSIKGALLAGLLLTQVQSISSLYISPVWSDPLLFGIMVLVLMWRPQGLFGK 289


Lambda     K      H
   0.328    0.145    0.413 

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: 262
Number of extensions: 18
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: 307
Length of database: 293
Length adjustment: 27
Effective length of query: 280
Effective length of database: 266
Effective search space:    74480
Effective search space used:    74480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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