GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citS in Klebsiella michiganensis M5al

Align Citrate:Na+ symporter, CitS (characterized)
to candidate BWI76_RS04430 BWI76_RS04430 citrate carrier protein

Query= TCDB::P31602
         (446 letters)



>FitnessBrowser__Koxy:BWI76_RS04430
          Length = 446

 Score =  829 bits (2141), Expect = 0.0
 Identities = 421/446 (94%), Positives = 440/446 (98%)

Query: 1   MTNMSQPPATEKKGVSDLLGFKIFGMPLPLYAFALITLLLSHFYNALPTDIVGGFAIMFI 60
           MTNMSQ P+ EKKGVSD+LGFKIFGMPLPLYAFALITLLLSHFYNALPTDIVGGFAIMFI
Sbjct: 1   MTNMSQAPSAEKKGVSDILGFKIFGMPLPLYAFALITLLLSHFYNALPTDIVGGFAIMFI 60

Query: 61  IGAIFGEIGKRLPIFNKYIGGAPVMIFLVAAYFVYAGIFTQKEIDAISNVMDKSNFLNLF 120
           IGA+FGEIGKRLPIFNKYIGGAPVMIFLVAAYFVYAGIFTQKEI+AI+NVMDKSNFLNLF
Sbjct: 61  IGAVFGEIGKRLPIFNKYIGGAPVMIFLVAAYFVYAGIFTQKEIEAITNVMDKSNFLNLF 120

Query: 121 IAVLITGAILSVNRRLLLKSLLGYIPTILMGIVGASIFGIAIGLVFGIPVDRIMMLYVLP 180
           IAVLITGAILSVNR+LLLKSLLGYIPTILMGI+GASIFGI IGL FGI VDRIMMLYVLP
Sbjct: 121 IAVLITGAILSVNRKLLLKSLLGYIPTILMGILGASIFGILIGLCFGISVDRIMMLYVLP 180

Query: 181 IMGGGNGAGAVPLSEIYHSVTGRSREEYYSTAIAILTIANIFAIVFAAVLDIIGKKHTWL 240
           IMGGGNGAGAVPLSEIYHSVTGRSREEYYSTAIAILTIANIFAIVFAA+LDIIGKKHTWL
Sbjct: 181 IMGGGNGAGAVPLSEIYHSVTGRSREEYYSTAIAILTIANIFAIVFAALLDIIGKKHTWL 240

Query: 241 SGEGELVRKASFKVEEDEKTGQITHRETAVGLVLSTTCFLLAYVVAKKILPSIGGVAIHY 300
           SGEGELVRKASFKVE+DEK GQITHRETAVGLVL+TTCFLLAYV+AKKILPSIGGV+IHY
Sbjct: 241 SGEGELVRKASFKVEDDEKAGQITHRETAVGLVLATTCFLLAYVIAKKILPSIGGVSIHY 300

Query: 301 FAWMVLIVAALNASGLCSPEIKAGAKRLSDFFSKQLLWVLMVGVGVCYTDLQEIINAITF 360
           FAWMVLIVAALNASGLCSPEIKAGAKRLSDFFSKQLLWVLMVGVGVCYTDLQEII+AITF
Sbjct: 301 FAWMVLIVAALNASGLCSPEIKAGAKRLSDFFSKQLLWVLMVGVGVCYTDLQEIIDAITF 360

Query: 361 ANVVIAAIIVIGAVLGAAIGGWLMGFFPIESAITAGLCMANRGGSGDLEVLSACNRMNLI 420
           ANVVIAA+IV+GAV+GAA+GGWL+GFFPIESAITAGLCMANRGGSGDLEVLSACNRMNLI
Sbjct: 361 ANVVIAAVIVVGAVVGAAVGGWLIGFFPIESAITAGLCMANRGGSGDLEVLSACNRMNLI 420

Query: 421 SYAQISSRLGGGIVLVIASIVFGMMI 446
           SYAQISSRLGGGIVLVIASIVFGMM+
Sbjct: 421 SYAQISSRLGGGIVLVIASIVFGMMM 446


Lambda     K      H
   0.327    0.144    0.420 

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: 808
Number of extensions: 31
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: 446
Length of database: 446
Length adjustment: 32
Effective length of query: 414
Effective length of database: 414
Effective search space:   171396
Effective search space used:   171396
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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