GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Sphingomonas koreensis DSMZ 15582

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases

Query= metacyc::MONOMER-11560
         (497 letters)



>FitnessBrowser__Korea:Ga0059261_1680
          Length = 469

 Score =  253 bits (646), Expect = 1e-71
 Identities = 163/460 (35%), Positives = 244/460 (53%), Gaps = 17/460 (3%)

Query: 35  ETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFADLL 94
           ETF  + P  GR  A       AD + AV  AR  F    W+      R A ++  AD +
Sbjct: 17  ETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPG--WAATPIEDRAAAILAIADSI 74

Query: 95  RKNVEELALLETLDMGKPIGDSSSIDIPGA---AQAIHWTAEAIDKVYDEVAPTPHDQLG 151
               +ELA L + + GKP+ ++   +I GA   A+A      A+D + D+ +        
Sbjct: 75  EAAKDELARLLSAEQGKPVPNAVG-EIMGALAWARATAGLRPAVDVLKDDDSVRVE---- 129

Query: 152 LVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEAG 211
            V R+P+GVV +I PWNFP+++A W + P L  GN+VV+KPS  +PL A+R+ ++A  A 
Sbjct: 130 -VHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAALRMVEIA-NAH 187

Query: 212 IPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKRIWLEAGGK 271
           +P GVLN + G    +G+A+A H  +D +VFTGST   + +M   G +N+KR+ LE GG 
Sbjct: 188 LPPGVLNSVTGEVE-IGRAIASHPGIDKIVFTGSTPTGRSIMA-DGAANLKRLTLELGGN 245

Query: 272 SPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALKGWKP 331
              IV  DA   + AA+  A A   N G++C A  R+ V  SI D     + E  +    
Sbjct: 246 DAAIVLPDADVDKVAAKIFAKAFG-NSGQICAAVKRVYVHESIHDALAEKLAEMARTAVV 304

Query: 332 GNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYVEPTIFDGV 391
           G   D  +  G + + +Q + V +  +     G + LAGG+    E  G +   ++   V
Sbjct: 305 GPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEA--REGDGYFFPLSVVVDV 362

Query: 392 TNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHKTARAVRAG 451
           T+ MRI  EE FGP+L VI +   E+A+A AN    GL   +W++D + A   A+ + AG
Sbjct: 363 TDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAFAQRLEAG 422

Query: 452 SVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
           +VWVN +       PFGG KQSG G +  L+ LE+Y +L+
Sbjct: 423 TVWVNDHASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQ 462


Lambda     K      H
   0.316    0.132    0.390 

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: 590
Number of extensions: 27
Number of successful extensions: 6
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: 497
Length of database: 469
Length adjustment: 34
Effective length of query: 463
Effective length of database: 435
Effective search space:   201405
Effective search space used:   201405
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: 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