GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Caulobacter crescentus NA1000

Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate CCNA_01204 CCNA_01204 dTDP-glucose 4,6-dehydratase

Query= SwissProt::A0R5C5
         (313 letters)



>FitnessBrowser__Caulo:CCNA_01204
          Length = 315

 Score =  125 bits (313), Expect = 2e-33
 Identities = 94/315 (29%), Positives = 144/315 (45%), Gaps = 19/315 (6%)

Query: 2   RTLVTGAAGFIGSTLVDRLLADGHGVVGLDDLSSGRAENLHSAENSDKFEFVKADIVDAD 61
           R LVTG AGF+GS L DRLL  G  V+ +D+  +G   N+    ++ +FE ++ D+    
Sbjct: 5   RILVTGGAGFVGSHLCDRLLETGAEVLCVDNYYTGSRLNVAQNLSNPRFELLRHDVT--- 61

Query: 62  LTGLLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAARLAGVRKVVHTSS 121
              +    + + I++LA   S      DP      +V G + +   A+   V+  +  +S
Sbjct: 62  ---MPLYVEVDQIYNLACPASPVHYQFDPVQTTKTSVHGAINMLGLAK--RVKAKILQAS 116

Query: 122 GGSVYGTPPAYPTSEDM-----PVNPASPYAAGKVAGEVYLNMYRNLYDLDCSHIAPANV 176
              VYG P  +P  E       P+   S Y  GK   E     Y   + L        N 
Sbjct: 117 TSEVYGDPTIHPQVESYWGNVNPIGLRSCYDEGKRCAETLFFDYWRQHKLRIKVARIFNT 176

Query: 177 YGPRQDPHGEAGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVDDVVDAFVR---AGGPAG 233
           YGPR  P+ +  VV+ F    L G    ++GDG+ TR + +VDD+VD  +R    G    
Sbjct: 177 YGPRMHPN-DGRVVSNFIVQALKGEDITLYGDGNQTRSFCYVDDLVDGLIRLMKTGDEVT 235

Query: 234 GGQRFNVGTGVETSTRELHTAIAGAVGAPDEPEFHPPRLGDLRRSRLDNTRAREVLGWQP 293
           G    N+G  VE + ++L   +    G+       P    D R+ + D T A++VL W P
Sbjct: 236 G--PINLGNPVEFTMKQLAELVLELTGSQSTIVHRPLPSDDPRQRQPDITLAKQVLDWTP 293

Query: 294 QVALAEGIAKTVEFF 308
              L  G+ KT+E+F
Sbjct: 294 TAPLKVGLMKTIEYF 308


Lambda     K      H
   0.317    0.136    0.396 

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: 258
Number of extensions: 13
Number of successful extensions: 4
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: 313
Length of database: 315
Length adjustment: 27
Effective length of query: 286
Effective length of database: 288
Effective search space:    82368
Effective search space used:    82368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 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