GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Rhodobacter viridis JA737

Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate WP_110805808.1 C8J30_RS10490 TRAP transporter large permease subunit

Query= reanno::SB2B:6938090
         (466 letters)



>NCBI__GCF_003217355.1:WP_110805808.1
          Length = 440

 Score =  400 bits (1027), Expect = e-116
 Identities = 226/473 (47%), Positives = 302/473 (63%), Gaps = 49/473 (10%)

Query: 1   MTIATLFLTLFLCMLLGMPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAI 60
           M+   +F  L   ML GMPI+I+LG + +  +   +   + +VALKL+    E + ++AI
Sbjct: 1   MSALIIFGLLIALMLTGMPISISLGLTVLTFLFTMTEVPIDTVALKLFTGI-EKFEIMAI 59

Query: 61  PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120
           PFFIL+  FL+ GGVA+R+I+FA   VGH  GGL +A V+AC LFAAVSGSSPATV AIG
Sbjct: 60  PFFILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIG 119

Query: 121 SIVIVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAAT--------------EV 166
           S+++  MV  G+P++F AGVITTSG LGILIPPSIVM++YA AT                
Sbjct: 120 SVILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPNGEAVSSA 179

Query: 167 SAARMFMAGLIPGLLMGVLLMVAIYIVARIKNLPSRPFPGVKALSLSSAKAMGGLALIFI 226
           S  ++FMAG++PGL++   L    +  AR    P      +     +  +A  GL LI +
Sbjct: 180 SVGQLFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLGQRFAAFREAFWGLMLIVV 239

Query: 227 VLGSIYGGVASPTEAAAVACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHV 286
           V+G IY G+ +PTEAAA++ VYA++++VF Y+D+  L++VP                   
Sbjct: 240 VIGGIYAGIFTPTEAAAMSAVYAFVISVFVYKDL-TLRDVP------------------- 279

Query: 287 GLGLIKTPTDKEIRNVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLP 346
                          V+   A +S MLL+II NA+LF+ ++  E IP  + E +V  GL 
Sbjct: 280 --------------RVLLSSANMSAMLLYIITNAVLFSFLMAHEGIPQALGEWMVNAGLS 325

Query: 347 PWGFLIIVNLLLLAAGNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLT 406
            W FLIIVN+LLLAAGNFMEPS+I+LIMAPILFP+AV+LGIDP+H GI++VVNME+GM  
Sbjct: 326 WWMFLIIVNVLLLAAGNFMEPSSIVLIMAPILFPVAVRLGIDPVHFGIMIVVNMEVGMCH 385

Query: 407 PPVGLNLFVTAGITGRSIGWVIHACLPWLLLLLGFLVLITYVPQISLFLPEYL 459
           PPVGLNL+V +GIT   I  +  A  PWLL +L FLVL+TYVP ISLFLP  L
Sbjct: 386 PPVGLNLYVASGITKMGITELTVAVWPWLLTMLVFLVLVTYVPTISLFLPHLL 438


Lambda     K      H
   0.329    0.144    0.424 

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: 622
Number of extensions: 33
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 466
Length of database: 440
Length adjustment: 33
Effective length of query: 433
Effective length of database: 407
Effective search space:   176231
Effective search space used:   176231
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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