GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Cupriavidus basilensis 4G11

Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate RR42_RS29650 RR42_RS29650 histidine ABC transporter permease

Query= reanno::pseudo6_N2E2:Pf6N2E2_2959
         (242 letters)



>FitnessBrowser__Cup4G11:RR42_RS29650
          Length = 229

 Score =  290 bits (742), Expect = 2e-83
 Identities = 146/225 (64%), Positives = 181/225 (80%)

Query: 16  LQGFGPLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLIRGVPD 75
           L GFGPLL+ GT  TI+LS LSL  +++LGLLGA+AKLS  + LR   + YTTLIR VPD
Sbjct: 3   LYGFGPLLLAGTIRTIELSLLSLATAIVLGLLGATAKLSFNRPLRELGRCYTTLIRSVPD 62

Query: 76  LVLMLLIFYSLQTWLTSLTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILSVPR 135
           LVLMLL+FYS+Q  + +LTD +     +IDPF AGV+TLGFIYGAYFTETFRGA LSVPR
Sbjct: 63  LVLMLLLFYSIQIGINNLTDAVGLPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFLSVPR 122

Query: 136 GQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQ 195
           GQ+EA  AYG+     FR ++FPQMMRFA+PGIGNNW V++KATALVSIIGLAD+VKAAQ
Sbjct: 123 GQLEAGAAYGMNGTLVFRRILFPQMMRFAIPGIGNNWQVLVKATALVSIIGLADIVKAAQ 182

Query: 196 DAGKSTYQLFYFLVLAALIYLLITSASNFILRWLERRYAAGAREA 240
           DAGKST+++F+F++ AA IYL+IT+ SN +L WL + Y++G R A
Sbjct: 183 DAGKSTFKMFFFILCAAFIYLVITTFSNLVLAWLAKHYSSGVRHA 227


Lambda     K      H
   0.329    0.142    0.418 

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: 203
Number of extensions: 4
Number of successful extensions: 1
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: 242
Length of database: 229
Length adjustment: 23
Effective length of query: 219
Effective length of database: 206
Effective search space:    45114
Effective search space used:    45114
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 (21.8 bits)
S2: 46 (22.3 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