GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Magnetospirillum magneticum AMB-1

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_011385142.1 AMB_RS13895 adenosylmethionine--8-amino-7-oxononanoate transaminase

Query= curated2:Q8TUZ5
         (389 letters)



>NCBI__GCF_000009985.1:WP_011385142.1
          Length = 439

 Score =  191 bits (485), Expect = 3e-53
 Identities = 142/432 (32%), Positives = 226/432 (52%), Gaps = 51/432 (11%)

Query: 1   MDARELIDKYHMNTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEA 60
           +DAR +   +     ++  +  +   G+ ++  +G EY+DLV+   VN+ GH +PA+ +A
Sbjct: 11  LDARHVWHPFTQAGTAQPAILALGARGSTIYAADGREYLDLVSSWWVNLHGHANPAIAQA 70

Query: 61  VKEQVERLIHCSNL-YYNEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF- 118
           V +Q  RL       + +EP A  A  + +  P DLN+VF+ + G+ +VE A+KLA ++ 
Sbjct: 71  VADQAGRLEQVIFADFTHEPAARLAHRVCKRLPGDLNRVFYSDDGSTAVEVALKLAHQYW 130

Query: 119 ----TGCTKFIAFEGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPY-----GDVNAV 169
                  + +IAFEGG+HG T GA+SA     +   ++ ++   E VP+     GD    
Sbjct: 131 RNHGQHRSTYIAFEGGYHGDTAGAMSAGHSSGYFGAWKEMLFPVETVPFPATWNGDETVE 190

Query: 170 EK------AID-------DDTAAVIVEP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIV 215
           +K      A+D       D  AAVI+EP +QG +G+R+    FLR+L     ++G LLI+
Sbjct: 191 DKEQAALDALDLLFAANPDHVAAVIIEPLIQGASGMRMCRPDFLRKLEAKVRDNGSLLIL 250

Query: 216 DEVQSGMGRTGQFFAFEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPGD---- 270
           DEV +G GRTG+ FA     + PD++CL+KGL GG +P+  T+AR+ + EAF   D    
Sbjct: 251 DEVMTGFGRTGEIFACVKAGITPDLICLSKGLTGGFLPLSVTVARDGIFEAFLGQDLSRA 310

Query: 271 --HGSTFGGNPLACAAVCAAV----STVLEENLP--EAAERKGKLAMRILSEAED----- 317
             HG ++  NPL CAA   ++    S   ++ +   EA  R+    ++ LS         
Sbjct: 311 FLHGHSYTANPLGCAAGLTSIDLLESAACQQRIGAIEAIHRRRLDGLKGLSNVAHTRLTG 370

Query: 318 --VVEEVRGRGLMMGVEVGDDERAKDVAREMLDRGALVNVTSGDVIRLVPPLVIGEDELE 375
                +V G G   G E G   + K      L+RG L+    G+V+ L+PP  I + ELE
Sbjct: 371 TVAALDVIGGG--KGYEAGIGPKLK---AAFLERGLLLR-PLGNVLYLLPPYCITDAELE 424

Query: 376 KALAELADALRA 387
           +A   + + LR+
Sbjct: 425 RAWDAVDEVLRS 436


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: 424
Number of extensions: 25
Number of successful extensions: 7
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: 439
Length adjustment: 31
Effective length of query: 358
Effective length of database: 408
Effective search space:   146064
Effective search space used:   146064
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.

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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