Alignments for a candidate for hom in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom in Pseudomonas stutzeri RCH2

Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate GFF3068 Psest_3126 Homoserine dehydrogenase

Query= SwissProt::Q5F8J4
         (435 letters)



>FitnessBrowser__psRCH2:GFF3068
          Length = 434

 Score =  496 bits (1278), Expect = e-145
 Identities = 253/435 (58%), Positives = 321/435 (73%), Gaps = 2/435 (0%)

Query: 1   MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAAFV 60
           MKPV +G+ GLGTVGGG   VL+ NAEEI+RR GR I ++ +       A+    +    
Sbjct: 1   MKPVKVGICGLGTVGGGTFNVLKRNAEEIARRAGRGIEVAQIAT-RHPNAKCDTGATPIT 59

Query: 61  KDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEK 120
            D F++V   ++D+VVEL GG  +AKE VLKAIENGKH+VTANK L+A +GNEIF  A +
Sbjct: 60  ADIFDVVNNPEIDIVVELIGGYTLAKELVLKAIENGKHVVTANKALIAVHGNEIFAKARE 119

Query: 121 QNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLK 180
           + VIV FEA+VAGGIP+IKA+REGLA NRI  +AGIINGT NFIL+EMREKG  F DVLK
Sbjct: 120 KGVIVAFEASVAGGIPVIKAIREGLAGNRINWLAGIINGTGNFILTEMREKGRTFEDVLK 179

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

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

Query: 301 GALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQAK 360
           G  PTASAVVAD++D+ R +  D  +RVPHLAFQP  +    ILP+    S+YYLR+QAK
Sbjct: 300 GMEPTASAVVADLVDVTRALTTDPNNRVPHLAFQPDSLSDHPILPISACESAYYLRIQAK 359

Query: 361 DEPGTLGQIAALLAQENVSIEALIQKGVIDQT-TAEIVILTHSTVEKHIKSAIAAIEALD 419
           D PG L Q+A++L++  ++IE+++QK   +Q     ++++TH  VE+ I  AIAA+E LD
Sbjct: 360 DHPGVLAQVASILSERGINIESIMQKEAEEQDGLVPVILVTHRVVEQRIDDAIAALEKLD 419

Query: 420 CVEKPITMIRMESLH 434
            V   +  IR+E L+
Sbjct: 420 DVADKVVRIRVEQLN 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: 541
Number of extensions: 10
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:

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