GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Marivita geojedonensis DPG-138

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_085635633.1 MGEO_RS04980 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::Q88RC0
         (480 letters)



>NCBI__GCF_002115805.1:WP_085635633.1
          Length = 476

 Score =  416 bits (1069), Expect = e-121
 Identities = 207/469 (44%), Positives = 302/469 (64%), Gaps = 3/469 (0%)

Query: 14  YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73
           YING W+   + +   V NPAT EV+ +V     A+   A++AA+ A+  W A T +ERS
Sbjct: 7   YINGTWVSGASKERFDVLNPATEEVLASVASAEIADADAALDAAEAAMAEWAARTPRERS 66

Query: 74  AKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPG 133
             LR+ +ELM    +D A+L+T E GK   +A GE  YAA F  WFAEEA R  G     
Sbjct: 67  EVLRKAWELMTVRLEDFAKLITLENGKARTDAMGEATYAAEFFRWFAEEAVRADGLITHA 126

Query: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALV 193
                R++V  +P G+   +TPWN+PAAM TRK  PALAAGC +++KPAS+TP + LAL+
Sbjct: 127 PASGARIMVQHKPAGLAVLVTPWNYPAAMGTRKIAPALAAGCAVIIKPASETPLTMLALM 186

Query: 194 ELAHRAGIPAGVLSVVTGS-AGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKV 252
            L   AG+P G+++V+     G +   +  +  VR +SFTGST +GR+L+   A  + K 
Sbjct: 187 PLLEEAGVPPGLVNVLPSKRTGALVDHMLHDPRVRVVSFTGSTGVGRKLLHSAADQVLKP 246

Query: 253 SLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAA 312
           ++ELGGNAP +VF+DAD+D A+EG +++K RN G+ C  ANRIYV + + + F ++L   
Sbjct: 247 AMELGGNAPVVVFEDADMDTAIEGTMLAKMRNLGEACTAANRIYVHEAIAETFTKRLTEK 306

Query: 313 VAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEGN--FFEPTI 370
           ++ LK+G+G++     GPL++ +   KV E + DAV+KGA +  GG   EG   ++ PT+
Sbjct: 307 MSALKVGDGIDPTVDVGPLVNAETRDKVAEFVADAVAKGAIIECGGTTPEGPGFYYPPTV 366

Query: 371 LVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEA 430
           L +VP+TA    +E FGP+A +  F+D+ EVI  +NDTE+GL +Y ++ DM R  +V E 
Sbjct: 367 LSNVPETADCVHDEIFGPVAAIQTFRDQEEVIRRANDTEYGLVAYVFSGDMKRALQVCER 426

Query: 431 LEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCIS 479
           L+YGMVG+N GL+S+  APFGG K SGLGREG   G+ +++E +Y+  S
Sbjct: 427 LDYGMVGLNRGLVSDPAAPFGGTKQSGLGREGGHEGMLEFMETQYISAS 475


Lambda     K      H
   0.317    0.134    0.384 

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: 588
Number of extensions: 20
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: 480
Length of database: 476
Length adjustment: 34
Effective length of query: 446
Effective length of database: 442
Effective search space:   197132
Effective search space used:   197132
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: 51 (24.3 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