Alignments for a candidate for hom in Flavobacterium glycines Gm-149

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom in Flavobacterium glycines Gm-149

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_066329102.1 BLR17_RS14640 bifunctional aspartate kinase/homoserine dehydrogenase I

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



>NCBI__GCF_900100165.1:WP_066329102.1
          Length = 815

 Score =  768 bits (1982), Expect = 0.0
 Identities = 389/814 (47%), Positives = 570/814 (70%), Gaps = 2/814 (0%)

Query: 1   MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60
           M+++KFGG+S+AN +NI+ V  I+  K++K+   +V SA   VT+ L   A+ A  ++ES
Sbjct: 1   MRVLKFGGTSVANAKNIKLVLDIVLNKAKKDKLIVVVSALSKVTDLLQLAASKAAANDES 60

Query: 61  YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120
           Y  I+ E+EK+HL+ +K+L+PV +QS+ L+ +K   N L  +  G +L+ E S RT D +
Sbjct: 61  YKEIVAEIEKKHLDALKELIPVSEQSSLLSHIKRIINHLETILDGCFLLGELSARTSDTI 120

Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHD 180
           LSFGE LS++I+A  L+     +SY D+R+L+KT++ +G A VNF+ TN L    F ++D
Sbjct: 121 LSFGELLSSYIIAEALKQNLKNSSYKDSRELIKTNNNYGKAAVNFEVTNSLTTAFFANND 180

Query: 181 -DIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVY 239
             + V+ GFI S+     TT+GR GSDYTA+I A AL A+++EIWTDV+G+ TA+P++V 
Sbjct: 181 AQVVVMPGFIASSLDEINTTLGRGGSDYTAAILAGALNADELEIWTDVNGMFTANPKIVK 240

Query: 240 TAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDS-G 298
            A  I  +SY EAMELSHFGAKV++P T+QP ++++IPI+IKNTF+P+  GT IS  S  
Sbjct: 241 QAQPIATISYQEAMELSHFGAKVLYPPTIQPVLRKNIPIHIKNTFEPEAEGTYISNVSVS 300

Query: 299 EGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICVA 358
            G  ++GIS +DNI+++ ++GPG++ V G S+R F  L+N GIN+I I+QASSEHSIC+ 
Sbjct: 301 NGIPVRGISHIDNITLITLEGPGMIGVSGSSKRLFEVLSNEGINVIFITQASSEHSICIG 360

Query: 359 IASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALG 418
           I + DA  A++ I + F  EI   ++D   +  ++ +IA+VGENM+++ G SGRMF  LG
Sbjct: 361 ILNSDAEVAENAINKAFEIEIAQNKIDPCIVEQNLCIIALVGENMKNHQGLSGRMFSTLG 420

Query: 419 RNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGKAL 478
           +NNVN+ AIAQG+SE NISAVI + D++KALN LHE FF  + K L+LF++GVG +G+  
Sbjct: 421 KNNVNIRAIAQGASERNISAVINERDVKKALNTLHENFFEENTKQLNLFVMGVGNVGEKF 480

Query: 479 TKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIGT 538
            + IHQQ K L+E   +++++  ++NSR M F ED  DL +     EN E  + + FI  
Sbjct: 481 IEQIHQQKKFLKENLKINVRVIALSNSRKMLFDEDAIDLNSWQAALENGETANKELFIEK 540

Query: 539 MTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQRG 598
           +  +N  NS+FVD TA+ DVA IYE+ L   VG+VT NK A +   + YK LKKL+ Q  
Sbjct: 541 VAALNLRNSIFVDITANADVAAIYERFLKQSVGVVTCNKIACASAYDNYKNLKKLSRQYN 600

Query: 599 VRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEVVAQA 658
             F +ETNV AGLP+I+T+++L+ SGD VH+I+AVLSGS+N+IF+  ++   F +VV +A
Sbjct: 601 APFLFETNVGAGLPIIDTVKNLIASGDKVHKIQAVLSGSLNFIFNNFDENNSFHDVVKEA 660

Query: 659 KEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEFFK 718
             +G+TEPDP+ DLSG+DVARKILIL RE+G  +  E++E  S +P  C    +  +FFK
Sbjct: 661 GVQGFTEPDPKIDLSGIDVARKILILIRESGYKMEIENIENNSFLPAACMATTNNEDFFK 720

Query: 719 KLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNMILFT 778
            L +++ HF+ +L EA AK  +L+F+A   NGKA VGL  +  +HPF+ L+G DN++LF 
Sbjct: 721 SLIEYNSHFEGILAEAKAKDSRLKFVAEFINGKANVGLQFIPKDHPFYNLEGKDNIVLFY 780

Query: 779 TERYNDFPMIVRGPGAGADVTAAGVFADIIRLGN 812
           T+RY D P++++G GAGA VTA+G+FAD+IR+GN
Sbjct: 781 TDRYVDQPLLIKGAGAGAAVTASGIFADVIRIGN 814


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: 1443
Number of extensions: 67
Number of successful extensions: 5
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: 815
Length adjustment: 41
Effective length of query: 774
Effective length of database: 774
Effective search space:   599076
Effective search space used:   599076
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 Jul 26 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:

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 2024 update 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 original 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