Alignments for a candidate for hom in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom in Polaromonas naphthalenivorans CJ2

Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_041376665.1 PNAP_RS11180 homoserine dehydrogenase

Query= SwissProt::Q5F8J4
         (435 letters)



>NCBI__GCF_000015505.1:WP_041376665.1
          Length = 440

 Score =  492 bits (1267), Expect = e-144
 Identities = 257/439 (58%), Positives = 321/439 (73%), Gaps = 6/439 (1%)

Query: 1   MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAAFV 60
           M P+ +GLLG+GTVG G   VL+ N EEI RR GR I I+ + DL   +A+ +      V
Sbjct: 1   MSPIRVGLLGIGTVGSGTFNVLKRNQEEIRRRAGRGIEITMVADLDVARAQALVGDGVLV 60

Query: 61  KDPF-ELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119
            D   ++VA  D+D+V+EL GG GIAK  VL+AIE+GKH+VTANK LLA +G EIF  A 
Sbjct: 61  VDDARKVVASPDIDIVIELIGGYGIAKALVLEAIESGKHVVTANKALLAVHGTEIFAAAH 120

Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179
           ++ V+V FEAAVAGGIPIIKALREGL+AN I+ IAGIINGT+NFILSEMR+KG  F  VL
Sbjct: 121 RKGVMVAFEAAVAGGIPIIKALREGLSANSIQWIAGIINGTTNFILSEMRDKGLDFGVVL 180

Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239
           KEAQ LGYAEADPTFDIEG DA HK T+MSA+AFG P+ F   Y+EGI+ L ++DI+YAE
Sbjct: 181 KEAQKLGYAEADPTFDIEGVDAAHKATLMSAIAFGIPVQFDKAYVEGITSLAAQDIRYAE 240

Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299
           +LGYRIKLLG+T++   GIELRVHP+LIP  RLLANV+G MNAV V+ D VG TLYYG G
Sbjct: 241 QLGYRIKLLGITKRVAGGIELRVHPSLIPAKRLLANVEGAMNAVVVHGDAVGTTLYYGKG 300

Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359
           AG+ PTASAV+AD++DI+RL  AD  HRVPHLAFQP ++    I+PM EI +SYYLR+  
Sbjct: 301 AGSEPTASAVIADLVDISRLHTADPEHRVPHLAFQPDEMSDLAIVPMSEIVTSYYLRLNV 360

Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVID-----QTTAEIVILTHSTVEKHIKSAIAA 414
            DE G L  +  +LA+  +SI+A++Q+   D      T  +++ILTH  VE  +  AIA 
Sbjct: 361 ADEAGVLASVTGILAEAGISIDAVLQREADDVGGEGSTQTDLIILTHDCVEAKMNEAIAQ 420

Query: 415 IEALDCVEKPITMIRMESL 433
           ++AL  V  PIT IR E L
Sbjct: 421 MQALPTVLAPITRIRKEEL 439


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: 525
Number of extensions: 20
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: 440
Length adjustment: 32
Effective length of query: 403
Effective length of database: 408
Effective search space:   164424
Effective search space used:   164424
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:

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