GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nbaE in Pseudomonas fluorescens FW300-N2E3

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate AO353_07805 AO353_07805 betaine-aldehyde dehydrogenase

Query= BRENDA::Q83XU8
         (485 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_07805 AO353_07805
           betaine-aldehyde dehydrogenase
          Length = 490

 Score =  334 bits (856), Expect = 5e-96
 Identities = 185/463 (39%), Positives = 269/463 (58%), Gaps = 8/463 (1%)

Query: 24  SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83
           +P N  V+A V  A  A+V+ AV +A+   K  W  M+  +R  +L    + +  R D+ 
Sbjct: 28  NPANGEVLATVQRATFADVERAVVSAEKGQK-IWAAMTAMERSRILRRAVEILRERNDEL 86

Query: 84  LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143
            A E  DTGK  S  R+VDI  GA   + +A +V  +  E   + T   V    Y  R P
Sbjct: 87  AALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIEGEQIPLRTTSFV----YTRREP 142

Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203
           +G+V  I  WN P+ +  WK  PALA GN ++ KPSE T  T   L E+   AG+P GV+
Sbjct: 143 LGIVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLKLAEIYTEAGLPAGVF 202

Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGA-RPVSLELGGKNAAIV 262
           NV+ G G    G +LT HP +  I+FTG T TG+ +M +A+  + + V++ELGGK+  I+
Sbjct: 203 NVLTGSG-REVGTWLTEHPRIEKISFTGGTDTGKKVMASASGSSLKDVTMELGGKSPLII 261

Query: 263 FADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDL 322
           F D DLD+A +  + + F + GQVC    RV+V   +   F +++ +    +++G PED 
Sbjct: 262 FDDADLDRAADTAMMANFYSSGQVCTNGTRVFVPSHLKAAFEAKIVERVARIRVGNPEDE 321

Query: 323 ATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDD 382
            T  GPL+S  H E VL Y  K  E GA ++ GG      E  KG A+V PT++T   D+
Sbjct: 322 NTNFGPLVSFAHMESVLGYIAKGKEEGARLLCGGERLTEGEFAKG-AFVAPTVFTDCTDE 380

Query: 383 SVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAW 442
             + REEIFGP   ++ +++EEEVIRRAND ++GLA  + T +L+RAHRV   +E GI W
Sbjct: 381 MTIVREEIFGPVMSILTYETEEEVIRRANDTEFGLAAGVVTRDLNRAHRVIHQLEAGICW 440

Query: 443 VNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485
           +N+W   D +   GG KQSG+GRE G+ SL  +T +K+V ++L
Sbjct: 441 INAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVEL 483


Lambda     K      H
   0.318    0.135    0.406 

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: 536
Number of extensions: 21
Number of successful extensions: 5
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: 485
Length of database: 490
Length adjustment: 34
Effective length of query: 451
Effective length of database: 456
Effective search space:   205656
Effective search space used:   205656
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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