GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Teredinibacter turnerae T7901

Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_015817208.1 TERTU_RS05175 homoserine dehydrogenase

Query= SwissProt::Q5F8J4
         (435 letters)



>NCBI__GCF_000023025.1:WP_015817208.1
          Length = 439

 Score =  464 bits (1195), Expect = e-135
 Identities = 240/441 (54%), Positives = 322/441 (73%), Gaps = 11/441 (2%)

Query: 1   MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAAFV 60
           MKPVN+G+ GLGTVG G   VL  N ++I+ + GREI+I+    +   + R+ C      
Sbjct: 1   MKPVNVGICGLGTVGSGTFNVLTRNNKDINAKAGREIKIT---HIGARRTREDCDLTGVT 57

Query: 61  --KDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLA 118
              D F +V   +VD++VEL GGT +AK+ VL+A+ NGKH+VTANK L+AEYGNE+F  A
Sbjct: 58  VSNDIFAVVNDPNVDILVELIGGTTVAKDLVLQAVRNGKHVVTANKALIAEYGNELFAEA 117

Query: 119 EKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADV 178
              NV + +EAAVAGGIPII++LREGLAAN+++ +AGIINGT NFIL+EMR+KG  F DV
Sbjct: 118 VSNNVTISYEAAVAGGIPIIRSLREGLAANKVEWLAGIINGTGNFILTEMRDKGRQFDDV 177

Query: 179 LKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYA 238
           LKEAQALGYAEADPTFD+EG DA HK+ I++++AFG P+ F   + EGIS++   D+ YA
Sbjct: 178 LKEAQALGYAEADPTFDVEGIDAAHKLVILASIAFGMPLQFDKVFTEGISQIRPEDVAYA 237

Query: 239 EELGYRIKLLGVTRK-TGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYG 297
           +ELGYRIK LG+TR+  GKGIELRVHPT+IP+SRLLANV+GVMNAV V  D VG TLYYG
Sbjct: 238 DELGYRIKHLGITRRLPGKGIELRVHPTMIPQSRLLANVNGVMNAVVVKGDAVGPTLYYG 297

Query: 298 AGAGALPTASAVVADIIDIARLVE----ADTAHRVPHLAFQPAQVQAQTILPMDEITSSY 353
           AGAGA PTASAV++DI+ ++R+V     ++ A  VPHL +    +   TILP++EI S+Y
Sbjct: 298 AGAGAEPTASAVISDIVHVSRMVNSSYVSEDATAVPHLGYGEDHLHDYTILPIEEIESAY 357

Query: 354 YLRVQAKDEPGTLGQIAALLAQENVSIEALIQKGVID-QTTAEIVILTHSTVEKHIKSAI 412
           YLR+ A D+PG L ++  + ++  +SIEALIQK   + Q    +++LT+ T+EK +  AI
Sbjct: 358 YLRLSALDQPGVLSRVTQIFSEAGISIEALIQKEPKEGQEHVSVILLTNRTIEKQVNKAI 417

Query: 413 AAIEALDCVEKPITMIRMESL 433
             IE+L  ++  +  IR+ESL
Sbjct: 418 EQIESLSPIQGNVVRIRVESL 438


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: 515
Number of extensions: 12
Number of successful extensions: 5
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: 439
Length adjustment: 32
Effective length of query: 403
Effective length of database: 407
Effective search space:   164021
Effective search space used:   164021
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 Apr 10 2024. The underlying query database was built on Apr 09 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:

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