GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Sphingobium czechense LL01

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_066609128.1 V473_RS20300 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_001046645.1:WP_066609128.1
          Length = 487

 Score =  489 bits (1259), Expect = e-143
 Identities = 251/475 (52%), Positives = 332/475 (69%), Gaps = 6/475 (1%)

Query: 51  SFVGGRWL--PTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKER 108
           +F+GG W+   + AT PV +PA+GA +GTV DCG  +  AA+ AA  AF +WK  +  +R
Sbjct: 15  AFIGGAWVGATSGATVPVDNPATGAIIGTVPDCGEADTLAAIAAAEAAFPAWKAQTAGDR 74

Query: 109 SSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIY 168
           +++L +W+ L++ N  +L +I+TAE GKP+ EA+GEI Y+A F++WF+EE RRV G I+ 
Sbjct: 75  AAVLERWHALVLANVADLGRIMTAEQGKPIAEAEGEIRYAASFIKWFAEEGRRVDGGIVP 134

Query: 169 TSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALAL 228
               ++R LV+K+PVGV++ ITPWNFP+AMITRK   ALAAGC VVVKP+E TP++ALAL
Sbjct: 135 APEANRRILVMKEPVGVSAAITPWNFPAAMITRKCAPALAAGCPVVVKPSELTPFTALAL 194

Query: 229 AQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSV 288
           A+LA +AGIP GV+N++    T    +G  L   P+V K+SFTGST  G +L+   A+++
Sbjct: 195 AKLAEEAGIPAGVFNIVTGLPT---AIGGALTASPVVRKLSFTGSTRVGSLLMRQCADTI 251

Query: 289 KRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKF 348
           KRVS ELGG AP IVFD A+VD AVA AM SKFRNAGQTCVC+NR LVQ G++D F  K 
Sbjct: 252 KRVSFELGGNAPLIVFDDADVDIAVASAMVSKFRNAGQTCVCANRILVQDGVYDQFAEKL 311

Query: 349 AEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGGNFF 408
           A A+  +L+V  G   G+T GPLIN  AVEKV+ HV DA++ GAT+        +G  F 
Sbjct: 312 ARAV-SALKVAPGDRTGSTIGPLINVAAVEKVQAHVEDALSHGATLFAQAANDATGARFA 370

Query: 409 EPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIWR 468
            P +L+  TRDM    EETFGPVAP+ +F  EEE + +ANA   GLA YFY+++  + +R
Sbjct: 371 TPVILTGATRDMRLAQEETFGPVAPLFRFTHEEEGIELANATSYGLAAYFYTENLHRAFR 430

Query: 469 VAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523
           VAE+LE GMV +N G I+    PFGGVK SGLGREG+  GI+EYLE K     GL
Sbjct: 431 VAERLEAGMVALNSGAIAMEVAPFGGVKMSGLGREGAHAGIEEYLETKAFHIAGL 485


Lambda     K      H
   0.318    0.135    0.400 

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: 638
Number of extensions: 23
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: 523
Length of database: 487
Length adjustment: 34
Effective length of query: 489
Effective length of database: 453
Effective search space:   221517
Effective search space used:   221517
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 24 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