GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_068166387.1 HTA01S_RS00735 homoserine dehydrogenase

Query= SwissProt::Q5F8J4
         (435 letters)



>NCBI__GCF_001592305.1:WP_068166387.1
          Length = 440

 Score =  493 bits (1268), Expect = e-144
 Identities = 255/440 (57%), Positives = 323/440 (73%), Gaps = 6/440 (1%)

Query: 1   MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQIC-PSAAF 59
           MKP+ +GLLG+GTVG G   VL+ N EEI RR GR I I+ + DL   +A+ I  P+   
Sbjct: 1   MKPIQVGLLGIGTVGSGTFNVLQRNQEEIRRRAGRGIEITMVADLDVARAQSIVGPNVKV 60

Query: 60  VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119
           V D   ++A  ++D+V+EL GG GIAK  V++AI  GKH+VTANK LLA +G EIF  A 
Sbjct: 61  VNDARAVIANPEIDIVIELIGGYGIAKALVMEAIAAGKHVVTANKALLAVHGTEIFAAAS 120

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

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

Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299
           +LGYRIKLLG+T++T KGIELRVHP+L+P  RL+ANV+G MNAV V  D VG TLYYG G
Sbjct: 241 QLGYRIKLLGITKRTDKGIELRVHPSLVPSKRLIANVEGAMNAVVVQGDAVGTTLYYGKG 300

Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359
           AG+ PTASAV+AD++DI RL  AD  HRVPHLAFQP ++   ++LPM E+ +SYYLR++ 
Sbjct: 301 AGSEPTASAVIADLVDITRLHTADPLHRVPHLAFQPDKMSDLSVLPMSEVVTSYYLRLRV 360

Query: 360 KDEPGTLGQIAALLAQENVSIEALIQK-----GVIDQTTAEIVILTHSTVEKHIKSAIAA 414
            DE G L ++  LLA   +SI+A++Q+     G    T+ +++ILTH T E  +   +A 
Sbjct: 361 ADEAGVLAKVTGLLANAGISIDAVLQREADEVGGEGATSTDLIILTHDTREGTMNEVLAQ 420

Query: 415 IEALDCVEKPITMIRMESLH 434
           ++AL  V  PIT IR E L+
Sbjct: 421 MQALPSVLAPITRIRKEELN 440


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: 490
Number of extensions: 13
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 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:

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