GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citA in Nocardiopsis lucentensis DSM 44048

Align Citrate:H+ symporter (characterized)
to candidate WP_017597434.1 D471_RS0103990 MFS transporter

Query= TCDB::P16482
         (444 letters)



>NCBI__GCF_000341125.1:WP_017597434.1
          Length = 433

 Score =  192 bits (489), Expect = 1e-53
 Identities = 120/381 (31%), Positives = 190/381 (49%), Gaps = 10/381 (2%)

Query: 36  GNFLEQFDFFLFGFYATYIAHT-FFPASSE-FASLMMTFAVFGAGFLMRPIGAIVLGAYI 93
           G  +E FDF+++   A  +  T FFP   +    LM +FA F  GF  RP+G +V G + 
Sbjct: 22  GTTIEWFDFYVYATAAGLVFGTLFFPGDIDPMVGLMASFATFAVGFFARPLGGVVFGHFG 81

Query: 94  DKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLLQGFSAGAELGGVSV 153
           D++GR+  L+ TL +M   TF + L+P+Y  +G  APLL+++ R +QG + G E GG  +
Sbjct: 82  DRLGRKSALVTTLLMMGVATFCVGLLPTYAQVGFVAPLLLVVLRFVQGIAVGGEWGGAVL 141

Query: 154 YLAEIATPGRKGFYTSW-QSGSQQVAIMVAAAMGFALNAVLEPSAISDWGWRIPFLFGVL 212
              E A   RK FY S+ Q G+   A++  A   F L    +   +  WGWR+PFL   L
Sbjct: 142 MAVESAPEERKTFYGSFAQLGNPAGALL--ATGSFGLITAWDSDLLYTWGWRLPFLASCL 199

Query: 213 IVPFIFILRRKLEETQEFTARRHHLAMR----QVFATLLANWQVVIAGMMMVAMTTTAFY 268
           +V    ++R K+EE+  F A R + A       +  TL  +W+ V+ G+ ++ +    +Y
Sbjct: 200 LVLVGLVVRLKVEESPVFEAARENRAAEPEGPPLRETLRTSWRAVLLGIGVLPVAVGGYY 259

Query: 269 LITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGRRSVLIAMTLLAL 328
           ++T +   +G     +S    L    L A    F       L DRFG   ++        
Sbjct: 260 VVTTFLQAYGVTEAGISEQLILSGLTLAAFVELFATLATAWLGDRFGTARIVTVGLAAVA 319

Query: 329 ATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEVRVAGFSLAYSL 388
             A P   +L    + L++L + L    +  +Y G +   L ++ P  VR  G S++Y +
Sbjct: 320 VLALPQFLVLETGSAVLIVLMLCLMRVAMAAVY-GPIARVLAQMYPPRVRYTGISVSYQV 378

Query: 389 ATAVFGGFTPVISTALIEYTG 409
           A A+FGG +P+  TAL   TG
Sbjct: 379 AGALFGGLSPLACTALFALTG 399


Lambda     K      H
   0.329    0.139    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: 526
Number of extensions: 29
Number of successful extensions: 6
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: 444
Length of database: 433
Length adjustment: 32
Effective length of query: 412
Effective length of database: 401
Effective search space:   165212
Effective search space used:   165212
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 (21.9 bits)
S2: 51 (24.3 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