Alignments for a candidate for hom in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom in Chlorobium phaeobacteroides BS1

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_012473759.1 CPHAMN1_RS01510 bifunctional aspartate kinase/homoserine dehydrogenase I

Query= reanno::Cola:Echvi_2000
         (815 letters)



>NCBI__GCF_000020545.1:WP_012473759.1
          Length = 819

 Score =  675 bits (1742), Expect = 0.0
 Identities = 354/819 (43%), Positives = 515/819 (62%), Gaps = 8/819 (0%)

Query: 1   MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60
           MK++KFGG+SI N E I+ V  II    +     +V SA   VT+ LL+ A  A   +  
Sbjct: 1   MKVLKFGGTSIENSERIRNVLGIIRGAIKDSPVIIVVSAIRKVTDLLLEAAVAAGSGDAG 60

Query: 61  YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120
           Y   L  +E  H ++V+ L+ + +++     +     ELGD+ +G+ L+++ S+R+   +
Sbjct: 61  YREKLVTIENIHGDLVRDLIDLSRRNEVQEVLTDELQELGDILYGVSLLRDLSDRSKALI 120

Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHD 180
           LSFGER S  I++     +G+  SY DAR L+ TD     A+V+   +++LI   FK   
Sbjct: 121 LSFGERFSARIISTFFCQEGLDASYTDARKLIVTDTNHCDARVDMSASSELISAWFKEER 180

Query: 181 DIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVYT 240
            + V+TG+IG+   G  TT+GR GSDYTA+I  +  GA++++IWTDV G  +ADP+ V  
Sbjct: 181 GVPVVTGYIGAAPDGTATTLGRGGSDYTATILGSVAGADEIQIWTDVDGFFSADPKRVKD 240

Query: 241 AFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRIS----KD 296
           A+ +P +SY EAMELSH GAKV+ P ++ PAMK+ IPI I+N++ PD  GTRIS     D
Sbjct: 241 AYVLPFISYGEAMELSHSGAKVLHPYSVHPAMKKGIPITIRNSYNPDVEGTRISAPEGND 300

Query: 297 SGEGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSIC 356
           +G GK + G+SS++++ +LN  G G+V V G++ R F  LA + INII ISQASSE SI 
Sbjct: 301 TGSGKPVTGLSSINDVVLLNFSGSGMVGVPGIASRLFSCLARHKINIIFISQASSEQSIS 360

Query: 357 VAIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQA 416
           +AI    A +A+ ++E+EF  E+   +++ +     +A+IAVVG+ M  +PG S  +F+ 
Sbjct: 361 LAINLVQAEKARLLLEQEFAAELAVRQIESLTFRKHIAIIAVVGKQMPGHPGVSAHLFET 420

Query: 417 LGRNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGK 476
           LG+N +NV A+AQG++E+NIS VI   D  KAL+ +HE+F LS  KV H+F+ G G I K
Sbjct: 421 LGKNGINVIAVAQGANEMNISFVIDSHDEDKALHCVHESFLLSRRKV-HVFIAGTGTIAK 479

Query: 477 ALTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLAT--VGPPDENDEPMDMDK 534
           +L   I      L++E  LD+ + GMAN+R     + G DL+    G     D     D 
Sbjct: 480 SLIGQIRDHSLTLRKEKELDVVVSGMANTRMHVSDDAGIDLSRWESGLKPRTDGKTVSD- 538

Query: 535 FIGTMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLA 594
           ++  +   N  N++FVDCTAS +VA  Y  +L S + +VT NK   +G  E Y+ + +  
Sbjct: 539 YVDYIKSRNLHNTIFVDCTASAEVAACYPDLLASNISVVTANKLGTAGSWELYETISEAL 598

Query: 595 GQRGVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEV 654
                RF YETNV AGLP+INTL DL  SGD + RIE VLSG+++YIF+EL KG  FSE+
Sbjct: 599 HASNARFLYETNVGAGLPIINTLNDLRNSGDRIVRIEGVLSGTLSYIFNELRKGRKFSEI 658

Query: 655 VAQAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVP 714
           V  A++ GYTEPDPR+DLSG D ARK LILGRE G  L +ED+E +S+VPE      SV 
Sbjct: 659 VRSARDAGYTEPDPREDLSGADFARKFLILGRELGYRLDYEDIECESLVPESLRGEMSVE 718

Query: 715 EFFKKLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNM 774
           EF ++L   D  +Q  + EA   G  + +   +  GKA++G+ +L   +P   L G++N+
Sbjct: 719 EFMERLGGIDAAYQTRISEAAETGMTIAYAGEISEGKARIGVKTLPVSNPVAGLNGTENL 778

Query: 775 ILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRLGNY 813
           ++FTT+RY D P++V+GPGAG +VTA GVFADI+R+ +Y
Sbjct: 779 VVFTTDRYLDTPLVVKGPGAGGEVTAGGVFADILRIASY 817


Lambda     K      H
   0.317    0.134    0.375 

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: 1412
Number of extensions: 53
Number of successful extensions: 6
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: 815
Length of database: 819
Length adjustment: 41
Effective length of query: 774
Effective length of database: 778
Effective search space:   602172
Effective search space used:   602172
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: 56 (26.2 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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