GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Lentibacillus jeotgali Grbi

Align lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_040912508.1 ON01_RS12160 aldehyde dehydrogenase family protein

Query= BRENDA::Q58806
         (463 letters)



>NCBI__GCF_000224785.1:WP_040912508.1
          Length = 481

 Score =  370 bits (949), Expect = e-107
 Identities = 193/468 (41%), Positives = 306/468 (65%), Gaps = 16/468 (3%)

Query: 3   IDGKWIN--REDMDVINPYSLEVIKKIPALSREEAKEAIDTA-EKYKEVMKNLPITKRYN 59
           I+G+ IN   + + V NPY+ + +++I  +S +  + A+  A + +   M+++P  KR +
Sbjct: 7   INGEEINTSNDSIKVKNPYNGDTVEEIALISDDAFERAVTGAFDTFHHTMQDMPAHKRSD 66

Query: 60  ILMNIAKQIKEKKEELAKILAIDAGKPIKQARVEVERSIGTFKLAAFYVKEHRDEVIP-- 117
           IL   A  ++E+ ++ A+ +  +AGKPI  +R EV+R+I   + A+   K    EV+P  
Sbjct: 67  ILRKTADLMEERADDFAETIMKEAGKPISFSRGEVQRAIQVLRFASEEAKHISGEVVPMD 126

Query: 118 ----SDDRLIFTRREPVGIVGAITPFNFPLNLSAHKIAPAIATGNVIVHHPSSKAPLVCI 173
                D RL   +  P+G+V AITPFNFPLNLS HKIAPAIA GN ++  P+   P+   
Sbjct: 127 AAIDGDGRLGLVKHIPLGVVAAITPFNFPLNLSLHKIAPAIAAGNTVIFKPAENTPVSAY 186

Query: 174 ELAKIIENALKKYNVPLGVYNLLTGAGEVVGDEIVVNEKVNMISFTGSSKVGELITKKAG 233
           +LAK+   A     +P GV NLL G+G++ G+++V ++KV+ ISFTGS  VG  I + AG
Sbjct: 187 KLAKLFHEA----GLPDGVLNLLMGSGDI-GEKLVTHDKVHKISFTGSLPVGRSIKESAG 241

Query: 234 FKKIALELGGVNPNIVLKDADLNKAVNALIKGSFIYAGQVCISVGMILVDESIADKFIEM 293
           FKK+ LELG  +PNI+  D ++N+AVN L+KG+F ++GQVCIS   I V +SI D+F++ 
Sbjct: 242 FKKVTLELGSNSPNIIFDDGNINEAVNKLVKGAFAFSGQVCISAQRIYVQKSIYDQFLKE 301

Query: 294 FVNKAKVLNVGNPLDEKTDVGPLISVEHAEWVEKVVEKAIDEGGKLLLGGKRDKALFYPT 353
           ++   + L +G+P  E+TD+GP+IS E A+  ++ ++ A++ G K+  GG+RD+ +  PT
Sbjct: 302 YIKATEDLTIGDPASEETDIGPMISEEEAKRAKEWIDDAVENGAKVATGGERDETILKPT 361

Query: 354 IL-EVDRDNILCKTETFAPVIPIIR-TNEEEMIDIANSTEYGLHSAIFTNDINKSLKFAE 411
           I+  V+ +  +   E FAP++ +I    EE+++  +N + YGL + +FT D+N++ + A+
Sbjct: 362 IMTNVESNMKIIADEVFAPIVSVIPFDTEEDVVGYSNDSIYGLQAGVFTKDVNRAFRVAD 421

Query: 412 NLEFGGVVINDSSLFRQDNMPFGGVKKSGLGREGVKYAMEEMSNIKTI 459
            LE GGV IN+ S +RQDN P+GGVK+SG+GREGVKYA++ M+  K I
Sbjct: 422 QLEMGGVWINEISTYRQDNHPYGGVKQSGVGREGVKYAVDGMTETKFI 469


Lambda     K      H
   0.317    0.137    0.381 

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: 601
Number of extensions: 29
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: 463
Length of database: 481
Length adjustment: 33
Effective length of query: 430
Effective length of database: 448
Effective search space:   192640
Effective search space used:   192640
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