GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Herbaspirillum seropedicae SmR1

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate HSERO_RS17580 HSERO_RS17580 hypothetical protein

Query= curated2:Q8TUZ5
         (389 letters)



>FitnessBrowser__HerbieS:HSERO_RS17580
          Length = 440

 Score =  237 bits (604), Expect = 6e-67
 Identities = 157/435 (36%), Positives = 228/435 (52%), Gaps = 57/435 (13%)

Query: 10  YHMNTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLI 69
           +H N  S+ P+  V GEG  + D +G  YID   G AV+ LGH HP V+EA+++QV  L 
Sbjct: 5   FHRNPRSKLPMA-VAGEGMELIDQDGKRYIDASGGAAVSCLGHGHPRVIEAIRKQVGELA 63

Query: 70  HCSNLYYNE-PQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF------TGCT 122
           +    ++   P  E A +LA+AAP  LN V+F + G+E+VE A+KLAR++          
Sbjct: 64  YAHTSFFTTAPAEELAAMLADAAPGSLNHVYFLSGGSEAVEAALKLARQYYVEVGQPQRR 123

Query: 123 KFIAFEGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVP-----------YGDVNAVEK 171
             IA    +HG T+GAL+       RE F P++ E  HV              DV  V++
Sbjct: 124 HIIARRQSYHGNTLGALAIGGNAWRREMFMPMLIEAHHVSPCYAYRNRADGESDVQYVQR 183

Query: 172 AID-----------DDTAAVIVEPVQGEAGVRIPPEG-FLRELRELCDEHGLLLIVDEVQ 219
             D           D   A + E V G     +PP G + R++R +CD++G+LLI+DEV 
Sbjct: 184 LADELEQKILSLGADQVIAFVAETVVGATAGAVPPVGDYFRKIRAVCDKYGVLLILDEVM 243

Query: 220 SGMGRTGQFFAFEHEDVLPDIVCLAKGLGGGV-PVGATIAREEVAEAFEPG----DHGST 274
           SGMGRTG  FA E + V+PDIV +AKGLG G  P+GA I  + + +A   G     HG T
Sbjct: 244 SGMGRTGYLFACEEDGVVPDIVVIAKGLGAGYQPIGAMICSDHIYDAVLRGSGFFQHGHT 303

Query: 275 FGGNPLACAAVCAAVSTVLEENLPEAAERKGKLAMRILSEA---EDVVEEVRGRGLMMGV 331
           + G+  ACAA  A   T+ EE L E   ++G+     L +A   +  V ++RGRGL +GV
Sbjct: 304 YIGHATACAAAVAVQKTIQEERLLENVRQRGEQLRSELRQAFGDQAHVGDIRGRGLFVGV 363

Query: 332 EVGDDERAK-----------DVAREMLDRGALV-------NVTSGDVIRLVPPLVIGEDE 373
           E+  +  +K            V  E + RG LV       +  +GD I L PP +   ++
Sbjct: 364 ELVAERSSKLPLSPDLRTHARVKAEAMKRGLLVYPMGGTIDGKNGDHILLAPPFIASSND 423

Query: 374 LEKALAELADALRAS 388
           + + +  L+DA+ AS
Sbjct: 424 ISEIVQRLSDAVAAS 438


Lambda     K      H
   0.318    0.137    0.405 

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: 401
Number of extensions: 25
Number of successful extensions: 6
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: 389
Length of database: 440
Length adjustment: 31
Effective length of query: 358
Effective length of database: 409
Effective search space:   146422
Effective search space used:   146422
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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