GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garD in Pedobacter sp. GW460-11-11-14-LB5

Align Galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (characterized)
to candidate CA265_RS19875 CA265_RS19875 altronate hydrolase

Query= SwissProt::P39829
         (523 letters)



>FitnessBrowser__Pedo557:CA265_RS19875
          Length = 548

 Score =  232 bits (591), Expect = 3e-65
 Identities = 171/532 (32%), Positives = 254/532 (47%), Gaps = 58/532 (10%)

Query: 16  IKVHDTDNVAIIVNDNGLKAGTRFPDGLELI--EHIPQGHKVALLDIPANGEIIRYGEVI 73
           +K+H  DNV + +  N  K  T   DG E I  + I   HK  + D+ A   II YG ++
Sbjct: 6   LKIHPNDNVLVALQ-NLAKGETVIYDGHEYILQDDIQAKHKFFMQDMNAGDHIIMYGVLV 64

Query: 74  GYAVRAIPRGSWIDESMVVLPEAP----PLHTLPLATKVPEPLPPLEGYTFEGYRNADGS 129
           G A   I +G  +D         P    P H    A  V +     EG TF GY  +DG 
Sbjct: 65  GKAQHFILKGGLMDTENTKHASDPYEFRPYHYEWHAPDVSK----FEGRTFNGYIRSDGR 120

Query: 130 VGTKNLLGITTSVHCVAGVVDYVVKIIERDL----LPKYP-------------------- 165
           VGT N      +V C    +D + + +  +L      KY                     
Sbjct: 121 VGTANYWLFIPTVFCENRNLDVIREALHNELGYAVTDKYKSYAHQLVEAYKNGEILAEAD 180

Query: 166 ----------------NVDGVVGLNHLYGCGVAINAPAAVVPIRTIHNISLNPNFGGEVM 209
                           NVDG+  LNH  GCG      AAV+  + +   + +PN  G V 
Sbjct: 181 PSSIGLANPSANRVFKNVDGIKFLNHQGGCG-GTRQDAAVLS-KLLAAYADHPNVAG-VT 237

Query: 210 VIGLGCEKLQPERLLTGTDDVQ-AIPVESASIVSLQDEKHVGFQSMVEDILQIAERHLQK 268
           V+ LGC+ LQ +  +   DD++   P     +   + ++    + +V++ ++     L +
Sbjct: 238 VLSLGCQNLQVKDFM---DDLKHRSPNFDKPLFVFEQQQSQSEEQLVKEAIRKTFIGLTE 294

Query: 269 LNQRQRETCPASELVVGMQCGGSDAFSGVTANPAVGYASDLLVRCGATVMFSEVTEVRDA 328
           +N+ +R+  P S+LV+G++CGGSD FSG++ANPAVGY SDLLV  G TV+ +E  E+  A
Sbjct: 295 INKIERQPAPLSKLVLGVKCGGSDGFSGISANPAVGYTSDLLVALGGTVLLAEFPELCGA 354

Query: 329 IHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGKTDRSANPSPGNKKGGLANVVEKALGSIA 388
              L  R  +E   ++ ++ M  Y+       +    NPSPGN K GL     K+ G+  
Sbjct: 355 EQQLIDRTKDETAARKFIQLMTAYNQSAENVGSGFFMNPSPGNIKDGLITDAIKSTGAAK 414

Query: 389 KSGKSAIVEVLSPGQRPTKRGLIYAATPASDFVCGTQQVASGITVQVFTTGRGTPYGLMA 448
           K G S + +VL   +  TK GL    TP +D    T + ASG T+ +FTTG GTP G   
Sbjct: 415 KGGTSPVEDVLDYTEPATKPGLNLVCTPGNDVEATTGKAASGATLILFTTGLGTPTGNPV 474

Query: 449 VPVIKMATRTELANRWFDLMDINAGTIATGEETIEEVGWKLFHFILDVASGK 500
            P IK++T   L  R  D++DIN G +  GE+TIE++G  +  + +  ASG+
Sbjct: 475 CPTIKVSTNNALTKRMGDIIDINCGPVIEGEKTIEQMGEDILEYCIKAASGE 526


Lambda     K      H
   0.317    0.136    0.403 

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: 735
Number of extensions: 37
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: 523
Length of database: 548
Length adjustment: 35
Effective length of query: 488
Effective length of database: 513
Effective search space:   250344
Effective search space used:   250344
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 (21.7 bits)
S2: 52 (24.6 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