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_066328676.1 BLR17_RS00255 bifunctional aspartate kinase/homoserine dehydrogenase I

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



>NCBI__GCF_900100165.1:WP_066328676.1
          Length = 803

 Score =  482 bits (1240), Expect = e-140
 Identities = 289/822 (35%), Positives = 480/822 (58%), Gaps = 31/822 (3%)

Query: 1   MKIIKFGGSSIANYENIQKVFSIIEQK-SEKEAFALVFSAFGGVTEQLLQCANIAQQSEE 59
           MKI+KFGG S++N E I KV SII  K ++ E  A+V SA G  T++L +   +A ++ +
Sbjct: 1   MKILKFGGKSLSNGEGINKVVSIITDKVNQGEKIAIVVSARGNATDELEEILAVASKNAD 60

Query: 60  SYHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDY 119
            Y ++L++ +K            QQ   A   +   F  L  LF G+ LI + S++  D 
Sbjct: 61  -YKSLLEQFKK-----------YQQDVYANVDLSEEFAVLDKLFEGVSLIGDYSSKIKDQ 108

Query: 120 VLSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSH 179
           +LS GE LS  +L A L  KG+   + D+R  +KTD +FG A+   + + K +  +FK +
Sbjct: 109 ILSIGELLSAKLLTAILVEKGVNARFADSRTFLKTDSKFGDAQPLEQVSKKNVIKYFKDN 168

Query: 180 DD-IKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLV 238
           DD + V+TGFIGS     TTT+GR+GS+YTAS+ A  L A++++ +T V G+ TA+P LV
Sbjct: 169 DDAVNVVTGFIGSNINNVTTTLGRNGSNYTASLLANYLDAKELQNYTHVDGIYTANPDLV 228

Query: 239 YTAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSG 298
             A  I  L++NEA EL++FGA ++   T+ P ++++IP+ I NTF  +  GT I+  S 
Sbjct: 229 ADAKKIDHLTFNEANELANFGATILHAKTIIPLLEKNIPLRILNTFNHENEGTLITATSK 288

Query: 299 EGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICVA 358
            G  IK +S +++++++N++G GL+   GV  R F  + +N I++ +ISQ SSE  I + 
Sbjct: 289 SGG-IKTLSVLEDLALVNLEGRGLLGKTGVDARIFKVMGDNNISVSIISQGSSERGIGLV 347

Query: 359 IASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALG 418
           +A   A++A   +E+EF  +  S ++++I +  D++VI+++G+++        R + AL 
Sbjct: 348 VAESQATKAMIELEKEFENDFYSKDVNKISVTDDVSVISIIGQDL----STFYRPYTALI 403

Query: 419 RNNVNVAAIAQGSSELNISAVITQADLQKALNALH-EAFFLSDYKVLHLFLVGVGLIGKA 477
           +N +         +  N+S V+ +++L KALN +H E F +S  K +++ + G GL+G  
Sbjct: 404 KNKIIPILFNNTVTGKNVSLVVKKSELNKALNVIHGEIFGVS--KKINIAVFGHGLVGGT 461

Query: 478 LTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIG 537
           L   I +  K +++   + + I  +ANS+ +  ++DG     V     N     +   I 
Sbjct: 462 LINQILESAKAIEKRKDIKLNIFAIANSKNVLLNKDGVSPNWVNEIQTNGFAYTIKDVIA 521

Query: 538 TMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQR 597
              E +  N + VD TAS    + Y  ++++   +++ NK AN+     YK+L+K+  + 
Sbjct: 522 YANENHLENLIAVDNTASAAFVENYIPLVENGFDLISSNKVANTLSYGFYKELRKVLAEN 581

Query: 598 GVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELE-KGMPFSEVVA 656
              + YETNV AGLP+I+T++ L LSG+++ +I+ V SG+++Y+F+    K  PFS+++ 
Sbjct: 582 QKNYLYETNVGAGLPLIDTIKLLHLSGENITKIKGVFSGTLSYLFNNFSAKDAPFSDILK 641

Query: 657 QAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEF 716
           +A + GYTEPDPR+DL G DV RK+LIL RE      FE++ IQ+++PE   +  S  +F
Sbjct: 642 EAIDNGYTEPDPREDLCGNDVGRKLLILARELDLQNEFEEIAIQNLIPEHLRE-GSAADF 700

Query: 717 FKKLQKHDGHFQQLLDEANAKGEKLRFMATL------ENGKAKVGLNSLDSEHPFFTLKG 770
             KL++ D  + ++ +E       LR++  L      + G  +V L S+ S+     LKG
Sbjct: 701 LTKLKEFDPIYTKIKEE-QKPNHVLRYIGELSGDLQNDKGILEVKLVSVPSDTALGGLKG 759

Query: 771 SDNMILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRLGN 812
           SD+     TE Y D P++++G GAG+ VTA GVF DI+RL +
Sbjct: 760 SDSFFEIYTESYGDRPIVIQGAGAGSAVTARGVFGDILRLSD 801


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: 1471
Number of extensions: 84
Number of successful extensions: 9
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: 803
Length adjustment: 41
Effective length of query: 774
Effective length of database: 762
Effective search space:   589788
Effective search space used:   589788
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