GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Sphingomonas koreensis DSMZ 15582

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__Korea:Ga0059261_1680
          Length = 469

 Score =  259 bits (663), Expect = 1e-73
 Identities = 158/473 (33%), Positives = 244/473 (51%), Gaps = 9/473 (1%)

Query: 7   TDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVP 66
           T  +L++DG+    A  +T  V++PATG+P      A  ADLD A+AAA+  F  W   P
Sbjct: 2   TGVRLIVDGK--PLAMAETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATP 59

Query: 67  AHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWF-ADEGRRVY 125
             +RAA +   A  +    D +A+L++ EQGKP+  A  E++ A   + W  A  G R  
Sbjct: 60  IEDRAAAILAIADSIEAAKDELARLLSAEQGKPVPNAVGEIMGA---LAWARATAGLRPA 116

Query: 126 GRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPA 185
             ++   +   +  V ++P+G VA+ +PWNFPV   +  +   L  G + ++K    TP 
Sbjct: 117 VDVLKDDD-SVRVEVHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPL 175

Query: 186 SPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGL 245
           +   ++    +A +P GV+  V G+  EI   +  HP I K+ FTGSTP G+ + +    
Sbjct: 176 AALRMVE-IANAHLPPGVLNSVTGE-VEIGRAIASHPGIDKIVFTGSTPTGRSIMADGAA 233

Query: 246 HMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTR 305
           ++KR T+ELGG+   IV  DADV           F N+GQ+C +  R  VH SI D    
Sbjct: 234 NLKRLTLELGGNDAAIVLPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAE 293

Query: 306 ALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNF 365
            L + A    VG G +  +  G + N ++   + ++ D+AR  G     GGE    +G F
Sbjct: 294 KLAEMARTAVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREGDGYF 353

Query: 366 FAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVH 425
           F  +V+ +V     + + E FGP+  +  +   E+A+A AN    GL G  ++   A   
Sbjct: 354 FPLSVVVDVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAAL 413

Query: 426 LLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478
              QRLE G +W+N  A+  P++PFGG K SG G+E G   LE Y+  ++V V
Sbjct: 414 AFAQRLEAGTVWVNDHASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTVRV 466


Lambda     K      H
   0.318    0.134    0.393 

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: 592
Number of extensions: 30
Number of successful extensions: 3
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: 481
Length of database: 469
Length adjustment: 33
Effective length of query: 448
Effective length of database: 436
Effective search space:   195328
Effective search space used:   195328
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: 51 (24.3 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