GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_1680 Ga0059261_1680
           NAD-dependent aldehyde dehydrogenases
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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