GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Acidimicrobium ferrooxidans DSM 10331

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_015798024.1 AFER_RS02935 aspartate aminotransferase family protein

Query= curated2:O30156
         (375 letters)



>NCBI__GCF_000023265.1:WP_015798024.1
          Length = 454

 Score =  182 bits (462), Expect = 2e-50
 Identities = 138/432 (31%), Positives = 208/432 (48%), Gaps = 66/432 (15%)

Query: 8   KKHILQTYTR-------QKVVIERGEGCYVYDVNGKRYLDLVAGIATVSIGHCNSHLVER 60
           ++H+   +TR       +  V+ RG+G YV+D  GKRYLD +AG+  V +GH  + L E 
Sbjct: 12  RRHLWMHFTRMASYDEHEVPVMVRGQGPYVWDSKGKRYLDGLAGLFVVQVGHGRTELAEA 71

Query: 61  LKEQLEKLIHISNLYYT-TPQVELAEKLSEIAGMD--RFFFCNSGAEAVEAALKFAR--- 114
             +Q  +L +     Y   P VELAE+L+ +A  D  R FF   G+EAVE+A K AR   
Sbjct: 72  ASKQASELAYFPLWSYAHQPAVELAERLAALAPGDINRVFFTTGGSEAVESAWKLARQYF 131

Query: 115 RATG---RKKFVSFTGDFHGRTMGALSVTHKEKFRKPFEPLV-----------------S 154
           + TG   + K +S    +HG +MGALS+T     + PFEPLV                 S
Sbjct: 132 KLTGQPTKTKVISRNLAYHGTSMGALSITGLPGIKTPFEPLVPGSIKVDNTNHYRCVHCS 191

Query: 155 PVEFAEFNNPESLEKVV----DEETAAVIVELVQGEAGVYPADREFVKAIEELREKYGFL 210
             E       + +E+ +     E  AAV +E VQ   G +     + + + E+ ++Y  L
Sbjct: 192 AAETCSLACADDIEQRILMEGPETVAAVFLEPVQNAGGCFTPAPGYFERVREICDRYDVL 251

Query: 211 LIVDEVQTGFGRTGRWFAKDHYGIEPDMITMAKAMGSGV-PIGCCALKEEVAEKIQVGD- 268
           L+ DEV TGFGR G WF    Y  +PD+IT AK M SG  PIG   + + + E       
Sbjct: 252 LVSDEVITGFGRLGEWFGAIRYDYQPDIITCAKGMTSGYSPIGAMLVSDRLMEPFLHDTT 311

Query: 269 ---HGSTFGGNPLACTAALATIEVIEREGLVENSARMGEYFVKRLKESFE-----NVIGV 320
              HG TF G+P++    LA +++ EREGL+++  R    F  +L    +      + G 
Sbjct: 312 TFLHGITFAGHPVSAAVGLANLDIFEREGLLDHVRRNEPLFRAQLDTLLDLPIVGEIRGA 371

Query: 321 GLMIG------------FDVGDAAEFVRKCL-----ENGLL--VNNTSERRIRLVPPLVI 361
           G   G            FD  ++   +R  L     E GL+   ++  +  ++L PPLV 
Sbjct: 372 GYFYGIELVKDRATRETFDDDESERLLRGILTPTLFELGLICRADDRGDPVVQLSPPLVA 431

Query: 362 TEREVDKAVEIM 373
              + ++ V I+
Sbjct: 432 GPEQFEEIVAIL 443


Lambda     K      H
   0.320    0.138    0.398 

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: 368
Number of extensions: 24
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: 375
Length of database: 454
Length adjustment: 31
Effective length of query: 344
Effective length of database: 423
Effective search space:   145512
Effective search space used:   145512
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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