Alignments for a candidate for hom in Paraburkholderia atlantica CCGE1002

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom in Paraburkholderia atlantica CCGE1002

Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_013089330.1 BC1002_RS06830 homoserine dehydrogenase

Query= SwissProt::Q5F8J4
         (435 letters)



>NCBI__GCF_000092885.1:WP_013089330.1
          Length = 443

 Score =  493 bits (1268), Expect = e-144
 Identities = 263/443 (59%), Positives = 319/443 (72%), Gaps = 9/443 (2%)

Query: 1   MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQI----CPS 56
           M+P+ +GLLG GTVG G   VLR N EEI RR GR I I+ +   +  KA         S
Sbjct: 1   MEPIKVGLLGFGTVGSGTFTVLRRNQEEIKRRAGRGIEIARIAVRNPAKATAALGAEAGS 60

Query: 57  AAFVKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFP 116
            A   D   +V    + +V E+ GGTGIA++ VL+AI NGKH+VTANK LLA +G EIF 
Sbjct: 61  VALTDDFNAVVDDPSISIVAEMIGGTGIARDLVLRAINNGKHVVTANKALLAVHGTEIFE 120

Query: 117 LAEKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFA 176
            A    V+V FEAAVAGGIPIIKALREGL ANRI+ IAGIINGT+N+ILSEMR++G  FA
Sbjct: 121 AARANGVMVAFEAAVAGGIPIIKALREGLTANRIQYIAGIINGTTNYILSEMRDRGLDFA 180

Query: 177 DVLKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIK 236
             LK AQ LGYAEADPTFDIEG DA HK TIMSA+AFG P+ F   Y+EGISKL + DIK
Sbjct: 181 TALKAAQELGYAEADPTFDIEGVDAAHKATIMSAIAFGVPVQFDRAYVEGISKLAAIDIK 240

Query: 237 YAEELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYY 296
           YAEELGYRIKLLG+TR+T KGIELRVHPTLIPE RLLANV+G MNAV V+ D VG TLYY
Sbjct: 241 YAEELGYRIKLLGITRRTDKGIELRVHPTLIPEKRLLANVEGAMNAVVVHGDAVGTTLYY 300

Query: 297 GAGAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLR 356
           G GAGA PTASAVVAD++D+ RL  AD  HRVPHLAFQP  +    ILP++E+TS YYLR
Sbjct: 301 GKGAGAEPTASAVVADLVDVTRLHTADPEHRVPHLAFQPDSLSNTPILPIEEVTSGYYLR 360

Query: 357 VQAKDEPGTLGQIAALLAQENVSIEALIQK--GVID---QTTAEIVILTHSTVEKHIKSA 411
           ++  D  G L  I  +LA   +SI+AL+QK   ++D   +   +I+++TH TVEK + +A
Sbjct: 361 LRVADVTGVLADITRVLADTGISIDALLQKESELVDANGKGETDILLITHETVEKQVNAA 420

Query: 412 IAAIEALDCVEKPITMIRMESLH 434
           I +IE L  V   +T +RME+L+
Sbjct: 421 IKSIEGLKTVVSQVTKLRMEALN 443


Lambda     K      H
   0.318    0.135    0.369 

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: 494
Number of extensions: 16
Number of successful extensions: 3
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: 435
Length of database: 443
Length adjustment: 32
Effective length of query: 403
Effective length of database: 411
Effective search space:   165633
Effective search space used:   165633
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: 51 (24.3 bits)

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

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis