GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Cupriavidus basilensis 4G11

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS14420 RR42_RS14420 branched-chain amino acid transporter permease subunit LivH

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__Cup4G11:RR42_RS14420
          Length = 308

 Score =  298 bits (764), Expect = 8e-86
 Identities = 150/302 (49%), Positives = 211/302 (69%), Gaps = 6/302 (1%)

Query: 4   FVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAG 63
           F QQL+NGLTLG+IY L+AIGYTMVYGIIGMINFAHG+I+M+G +  L+  L      AG
Sbjct: 8   FTQQLVNGLTLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIGAYVGLVT-LTAIGASAG 66

Query: 64  LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQ 123
            P+ ++L   L+V++L+T L+ + +ERVAYRPLRG  RL PLI+AIGMSI L N++Q+ Q
Sbjct: 67  YPLPLVLGAALLVSVLVTGLYGFAVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQIGQ 126

Query: 124 GPRNKPIPPMVSSVYQFG-----NISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRA 178
           G R+  +P ++S   +F       ++V   +++I+ +T VL+      +  + +GRA RA
Sbjct: 127 GARDMSVPVLISGAIEFQMGSDFTVTVPYSRLLIVGVTLVLMLALTLFIGHSRMGRACRA 186

Query: 179 TEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAA 238
             +D +MA LLG++ ++ IS TFV+GA LAAV G +  +  G  +   GF  G+KAFTAA
Sbjct: 187 CAEDMRMANLLGIDTNRVISFTFVLGAMLAAVGGVLIGLTIGKLNPYIGFVAGIKAFTAA 246

Query: 239 VLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVE 298
           VLGGIGS+PGA+ GG+L+GL E+  S Y    YKDV  F +L  +L+F+PTG+LG+P+VE
Sbjct: 247 VLGGIGSIPGAMLGGVLLGLAETFASGYMPAEYKDVVAFGLLVLILLFRPTGLLGKPDVE 306

Query: 299 KV 300
           KV
Sbjct: 307 KV 308


Lambda     K      H
   0.329    0.143    0.421 

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: 382
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: 300
Length of database: 308
Length adjustment: 27
Effective length of query: 273
Effective length of database: 281
Effective search space:    76713
Effective search space used:    76713
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: 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