GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Pseudomonas fluorescens FW300-N2C3

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate AO356_13795 AO356_13795 betaine-aldehyde dehydrogenase

Query= BRENDA::Q83XU8
         (485 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_13795
          Length = 490

 Score =  337 bits (863), Expect = 7e-97
 Identities = 187/463 (40%), Positives = 270/463 (58%), Gaps = 8/463 (1%)

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

Query: 84  LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143
            A E  DTGK  S  R+VDI  GA   + +A +V  +  E  ++P  D   +  Y  R P
Sbjct: 87  AALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIEGE--QIPLRDT--SFVYTRREP 142

Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203
           +GVV  I  WN P+ +  WK  PALA GN ++ KPSE T  T   L E+   AGVP GV+
Sbjct: 143 LGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLKLAEIYTEAGVPAGVF 202

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

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

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

Query: 383 SVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAW 442
             + REEIFGP   ++ +D+EEEVIRRAND D+GLA  + T +L+RAHR+   +E GI W
Sbjct: 381 MTIVREEIFGPVMSILTYDTEEEVIRRANDTDFGLAAGVVTRDLNRAHRIIHQLEAGICW 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: 543
Number of extensions: 20
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 (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