GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Caulobacter crescentus NA1000

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate CCNA_00664 CCNA_00664 C4-dicarboxylate transport protein

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__Caulo:CCNA_00664
          Length = 417

 Score =  513 bits (1322), Expect = e-150
 Identities = 252/409 (61%), Positives = 334/409 (81%), Gaps = 1/409 (0%)

Query: 7   KSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMES 66
           KS+Y QVL AI +G+L+G  +P+IG  +KPLGDGF+KLIK++IAPVIFCTV  GIA M  
Sbjct: 2   KSIYVQVLIAIVLGVLVGAIWPQIGVALKPLGDGFIKLIKLVIAPVIFCTVAGGIARMGD 61

Query: 67  MKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKD 126
           MKA GR G  AL+YFE+VST+AL+IGL++  ++QPGAG N+DPATLDA   A Y ++A+ 
Sbjct: 62  MKAFGRVGVKALIYFEVVSTLALVIGLVVGRLIQPGAGFNIDPATLDASIAAGYVEKAQH 121

Query: 127 -QGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVI 185
            +G+VA+++ +IP + IGAFA GN+LQVL+ A+L GFA  R+G  G+ + +V++  S++ 
Sbjct: 122 GEGMVAYLLHLIPDTFIGAFADGNLLQVLVIAILTGFACVRMGDFGEKVAHVLDETSKLF 181

Query: 186 FGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKAT 245
           FGII++++RLAPIGAFGAM FTIGKYGV  LVQLG L+  FY+T +LFV++VLG IA  +
Sbjct: 182 FGIIHIVVRLAPIGAFGAMGFTIGKYGVEALVQLGALVATFYVTSLLFVLVVLGGIAWVS 241

Query: 246 GFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT 305
           GFSIF+F+ YIREELLIVLGTSSSES LP+M++K+E  G R+SVVGLVIPTGYSFNLDGT
Sbjct: 242 GFSIFRFLAYIREELLIVLGTSSSESVLPQMMEKLENAGARRSVVGLVIPTGYSFNLDGT 301

Query: 306 SIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP 365
           +IY+T+A +F+AQATN+ + +  ++ LL V +L+SKGA+GVTG+GFI LAATL+ V  +P
Sbjct: 302 NIYMTLATLFLAQATNTPLSLGQELALLGVAMLTSKGASGVTGAGFITLAATLAVVPDIP 361

Query: 366 VAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVL 414
           +A LA+++G+DRFMSE RALTNLVGNGVAT+VVA+W   LD ++LD VL
Sbjct: 362 IAALAILVGVDRFMSECRALTNLVGNGVATLVVARWEGALDRQRLDRVL 410


Lambda     K      H
   0.327    0.142    0.401 

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: 611
Number of extensions: 30
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: 428
Length of database: 417
Length adjustment: 32
Effective length of query: 396
Effective length of database: 385
Effective search space:   152460
Effective search space used:   152460
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: 50 (23.9 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