GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Dinoroseobacter shibae DFL-12

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 3608039 Dshi_1446 aminotransferase class-III (RefSeq)

Query= curated2:Q8TUZ5
         (389 letters)



>FitnessBrowser__Dino:3608039
          Length = 444

 Score =  212 bits (540), Expect = 1e-59
 Identities = 146/421 (34%), Positives = 213/421 (50%), Gaps = 56/421 (13%)

Query: 21  TLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHC-SNLYYNEP 79
           T V G G  + D +G  Y+D   G AV+ LGH HPAV  A+  Q++++    +  + +EP
Sbjct: 15  TAVAGAGCYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQIDKIAFAHTGFFTSEP 74

Query: 80  QAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCT------KFIAFEGGFHG 133
                  L  AAPK + KV+  + G+ESVE A+KLAR+F   T      + IA    +HG
Sbjct: 75  AEVLCDALIAAAPKGIEKVYLLSGGSESVEAALKLARQFFLETGEPRRHRVIARRQSYHG 134

Query: 134 RTMGALSATWKPEFREPFEPLVPE---------FEHVPYGDVNA-------------VEK 171
            T+GAL+A      RE + PL+ E         + H   G+ +A             +E+
Sbjct: 135 NTLGALAAGGNAWRREKYAPLLVETYHIDPCYAYRHQAVGESDAAYGRRAADALRTEIER 194

Query: 172 AIDDDTAAVIVEPVQGEAGVRIPPE-GFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFA 230
              +   A I EPV G     +PP  G+   +RE+CDE+G+LLI+DEV  GMGRTG  FA
Sbjct: 195 LGPETVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILDEVMCGMGRTGTLFA 254

Query: 231 FEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPG----DHGSTFGGNPLACAAV 285
            E + + PDIV +AKGLG G  P+GA +A   + +A   G     HG T+ G+PLA AA 
Sbjct: 255 CEQDGISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGSGSFQHGHTYHGHPLAAAAA 314

Query: 286 CAAVSTVLEENLPEAAERKGKLAMRILSEA---EDVVEEVRGRGLMMGVEVGDD---ERA 339
            A V T+           KG      L  A      V ++RGRGL  G+E+ +D   +R 
Sbjct: 315 GAVVETLRAPGTMAQVRAKGATLQSRLEAALGQHSHVGDIRGRGLFRGIELVEDRDTKRP 374

Query: 340 KDVAREM--------LDRGAL-------VNVTSGDVIRLVPPLVIGEDELEKALAELADA 384
            D AR++        + RG +       ++   GD I L PP +I + +++  +  LA+A
Sbjct: 375 LDPARKVSARIKAAAMARGLICYPGSGTIDGKHGDHILLAPPFIIEDKQIDALVHMLAEA 434

Query: 385 L 385
           +
Sbjct: 435 I 435


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: 436
Number of extensions: 23
Number of successful extensions: 9
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: 444
Length adjustment: 31
Effective length of query: 358
Effective length of database: 413
Effective search space:   147854
Effective search space used:   147854
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