GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Pseudomonas putida KT2440

Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate PP_1470 PP_1470 Homoserine dehydrogenase

Query= SwissProt::Q5F8J4
         (435 letters)



>FitnessBrowser__Putida:PP_1470
          Length = 434

 Score =  497 bits (1279), Expect = e-145
 Identities = 251/435 (57%), Positives = 324/435 (74%), Gaps = 2/435 (0%)

Query: 1   MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAAFV 60
           MKPV +G+ GLGTVGGG   VL+ NAEEI+RR GR I ++ +   S+    QI       
Sbjct: 1   MKPVKVGICGLGTVGGGTFNVLQRNAEEIARRAGRGIEVAQIAMRSQNPNCQIT-GTPIT 59

Query: 61  KDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEK 120
            D FE+ +  ++D+V+EL GG  IA++ VLKAIENGKH+VTANK L+A +GNEIF  A +
Sbjct: 60  ADVFEVASNPEIDIVIELIGGYTIARDLVLKAIENGKHVVTANKALIAVHGNEIFAKARE 119

Query: 121 QNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLK 180
           + VIV FEAAVAGGIP+IKA+REGL+ANRI  +AGIINGT NFIL+EMREKG AF DVL 
Sbjct: 120 KGVIVAFEAAVAGGIPVIKAIREGLSANRINWLAGIINGTGNFILTEMREKGRAFPDVLA 179

Query: 181 EAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAEE 240
           EAQALGYAEADPTFD+EG DA HK+TI++++AFG P+ F   Y EGI++L + D+ YAE 
Sbjct: 180 EAQALGYAEADPTFDVEGIDAAHKLTILASIAFGIPLQFDKAYTEGITQLTTADVNYAEA 239

Query: 241 LGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAGA 300
           LGYRIK LGV R+T +GIELRVHPTLIP  RL+ANV+GVMNAV VN D  G TLYYGAGA
Sbjct: 240 LGYRIKHLGVARRTAEGIELRVHPTLIPADRLIANVNGVMNAVMVNGDAAGSTLYYGAGA 299

Query: 301 GALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQAK 360
           G  PTAS+VV D++D+ R + +D  +RVPHLAFQP  + A  ILP++   S+YYLR+QAK
Sbjct: 300 GMEPTASSVVGDLVDVVRAMTSDPENRVPHLAFQPDSLSAHPILPIEACESAYYLRIQAK 359

Query: 361 DEPGTLGQIAALLAQENVSIEALIQKGVIDQT-TAEIVILTHSTVEKHIKSAIAAIEALD 419
           D PG L Q+A++L++  ++IE+++QK   +Q     ++++TH  VE+ I  AI A+EAL 
Sbjct: 360 DHPGVLAQVASILSERGINIESIMQKEAEEQDGLVPMILVTHGVVEQRINDAIVALEALQ 419

Query: 420 CVEKPITMIRMESLH 434
            V   +  IR+E L+
Sbjct: 420 DVVGKVVRIRVEQLN 434


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: 539
Number of extensions: 14
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: 434
Length adjustment: 32
Effective length of query: 403
Effective length of database: 402
Effective search space:   162006
Effective search space used:   162006
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 09 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