GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Caulobacter crescentus NA1000

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate CCNA_01892 CCNA_01892 short chain dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__Caulo:CCNA_01892
          Length = 546

 Score =  137 bits (346), Expect = 4e-37
 Identities = 95/257 (36%), Positives = 136/257 (52%), Gaps = 16/257 (6%)

Query: 18  RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77
           + +++VVL+TG A GIG A    FA    +++++D   E+    A      G D HA+  
Sbjct: 29  KAQSRVVLVTGGADGIGWAACQRFARAGDQVLVADRNVERARERAD---SLGPDHHAIAM 85

Query: 78  DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDP-----LEMTEEDWRRCFAIDLDG 132
           DVS++  +           GR+DVLVN AGV    DP     L+ T E+  R  AI++ G
Sbjct: 86  DVSSEAQIREGFEQLHREFGRLDVLVNNAGVT---DPQPTATLDQTAEEVARLQAINVTG 142

Query: 133 AWYGCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKG 192
           A+   +     MIEQG G+IIN+AS      +     Y  +K  ++ LTR L  E+A KG
Sbjct: 143 AFLAAREAGRLMIEQGHGAIINLASGAGLVALAKRTSYSASKAAVISLTRTLACEWAAKG 202

Query: 193 VRVNAIAPGYIETQLNVDYWN-GFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDE 251
           VRVNA+ PGY  TQ+  D  + G  DP     R     P  R+G+P E+A  A FLASD 
Sbjct: 203 VRVNAVLPGYTRTQMVQDQIDAGLLDPSIVLSRI----PLGRMGEPEEMAEGAFFLASDA 258

Query: 252 APFINASCITIDGGRSV 268
           A ++  + + +DGG +V
Sbjct: 259 ASYVVGATLVVDGGYTV 275



 Score =  122 bits (307), Expect = 1e-32
 Identities = 90/265 (33%), Positives = 136/265 (51%), Gaps = 16/265 (6%)

Query: 4   PLSLPPVPEPPKGERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAA 63
           P S  P P P        +V  +TG  +GIG  +V  F +   RL++ +  AE  + +A 
Sbjct: 281 PASTTPAPSPLAPSP---RVSAITGGGRGIGRCVVDLFHAAGDRLLVIERDAEGAKALA- 336

Query: 64  HWRERGADVH-ALKADVSNQQDLHAMARHAVERHGRIDVLVNCAGV-NVFRDPLEMTEED 121
              E   D H  ++AD+++   + A    A  R GR+DVL+N AG  +VF+  LE T +D
Sbjct: 337 ---EALGDEHIVVQADITDVAAVEAAFAQAQARWGRLDVLINNAGAADVFKPSLEQTAQD 393

Query: 122 WRRCFAIDLDGAWYGCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLT 181
           +   + ++  G     KA    M + GV  I+N+ S      +P    Y  AK  +  ++
Sbjct: 394 FTSVYDLNFSGPLATAKAAARLMSQGGV--IVNLGSIAGLGALPQRNAYCAAKAAVTMMS 451

Query: 182 RALGIEYAPKGVRVNAIAPGYIETQLNVDYWN-GFADPYAERQRALDLHPPRRIGQPIEV 240
           R+L  E+A  G+RVN +APGYIET   +   + G A     R+RA    P  R+G P+EV
Sbjct: 452 RSLACEWASAGIRVNTVAPGYIETPAVLALKSAGRAQFDKIRRRA----PIGRLGDPMEV 507

Query: 241 AMTAVFLASDEAPFINASCITIDGG 265
           A T  FLAS  A ++  + +T+DGG
Sbjct: 508 ARTIAFLASPAASYVAGATLTVDGG 532


Lambda     K      H
   0.321    0.137    0.419 

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: 348
Number of extensions: 19
Number of successful extensions: 9
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: 272
Length of database: 546
Length adjustment: 30
Effective length of query: 242
Effective length of database: 516
Effective search space:   124872
Effective search space used:   124872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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