GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Lacinutrix algicola AKS293

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_055437364.1 ASC41_RS14495 bifunctional aspartate kinase/homoserine dehydrogenase I

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



>NCBI__GCF_001418085.1:WP_055437364.1
          Length = 814

 Score =  722 bits (1863), Expect = 0.0
 Identities = 370/814 (45%), Positives = 560/814 (68%), Gaps = 3/814 (0%)

Query: 1   MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60
           M+++KFGG+S+ + +NI KV +I+E  S+K+    V SA GG+T++LL+  N+A+ + ++
Sbjct: 1   MQVLKFGGTSVGSSKNINKVITILEDYSKKDKVICVVSAVGGITDKLLKAGNLAKDNNKN 60

Query: 61  YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120
           Y T  + ++ +H++++++L+P Q  +  +  +  +  +L +L  GI+LI E S +T D +
Sbjct: 61  YKTEYKSIKAKHIKVLEELIP-QNNAAIIKELDGKLKKLKNLLDGIFLINELSPQTSDRL 119

Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHF-KSH 179
           +SFGE LS+FI+A  L+++G+     + + L+ T+  +  A+V F+TTN  IQ++F ++ 
Sbjct: 120 VSFGELLSSFIIAETLKSRGVNAVRKNTQQLIVTNSNYTKAEVIFETTNNNIQEYFNEAT 179

Query: 180 DDIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVY 239
            DI ++ GFI  +  G+TTT+GR GSDYTA+I AAAL  E++EIWTDVSG+ T +P+LV 
Sbjct: 180 QDITLLPGFISKSYLGKTTTLGRGGSDYTAAIVAAALKTERLEIWTDVSGMYTTNPKLVK 239

Query: 240 TAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSG- 298
            A+ I ++SY+EAMELSHFGAKV++P T+QP +  +IPI+IKNT KP+E GT IS +   
Sbjct: 240 QAYPIERISYHEAMELSHFGAKVLYPPTVQPVLSLNIPIHIKNTLKPNEFGTIISNEGNT 299

Query: 299 EGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICVA 358
           +     GI+++++I++L +QG G+V + G S+R F TL+   INIILI+QASSEHSIC  
Sbjct: 300 KSSTATGITNINDIALLTLQGNGMVGIPGFSKRLFETLSQEKINIILITQASSEHSICFG 359

Query: 359 IASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALG 418
           I+  DA +A++ I   F +EI    +D I +  ++++IA+VG+NM+ + G SG+MF ALG
Sbjct: 360 ISKDDAIQAETAINLAFEHEISKHRIDPITVEQNLSIIALVGDNMKSHQGISGKMFSALG 419

Query: 419 RNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGKAL 478
           +NN+N+ AIAQG+SE NISAVI + D++KALN +HE FF ++ K L++F+ G+G +G+ L
Sbjct: 420 KNNINIRAIAQGASERNISAVIAEKDVEKALNTIHERFFGNNIKQLNVFITGIGNVGEKL 479

Query: 479 TKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIGT 538
              IHQQ   L++   LD++I GMANS+ M F+ +G DL        + +   +D F+  
Sbjct: 480 IDQIHQQSNYLKKNLKLDVRIVGMANSKKMIFNAEGIDLNDWASKFHHADKSTLDGFLEK 539

Query: 539 MTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQRG 598
              +N  NS+FVD TA+  V+ +YE  L S + +V  NK A S     YK L+ LA +  
Sbjct: 540 AKALNLRNSIFVDITANDAVSKMYEHYLRSSIAVVACNKIACSSTYSNYKLLQDLALKYN 599

Query: 599 VRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEVVAQA 658
             FFYETNV AGLP+INTL +L+ SGD V  I+AVLSGS+N++F+       F + V +A
Sbjct: 600 TPFFYETNVGAGLPIINTLNNLVSSGDKVTSIQAVLSGSLNFVFNNFSDKTNFHDTVKRA 659

Query: 659 KEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEFFK 718
           + +GYTEPDPR DLSG+DVARKILIL RE G  +  E +E  S + +   ++ +V +F+K
Sbjct: 660 QFEGYTEPDPRIDLSGIDVARKILILARENGGAMEIESIENDSFLTKANLESDTVDDFYK 719

Query: 719 KLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNMILFT 778
            L+  + HFQ+L   A AK  +L+++A  +NGKAKVGL  +   HPF+ L+G DN+++F 
Sbjct: 720 TLKTEEAHFQKLYASAKAKNCQLKYVAEFKNGKAKVGLKEIPEGHPFYNLEGKDNIVMFY 779

Query: 779 TERYNDFPMIVRGPGAGADVTAAGVFADIIRLGN 812
           TERY + P+IV+G GAGADVTA+G+FADII+ G+
Sbjct: 780 TERYPEQPLIVKGAGAGADVTASGLFADIIKAGS 813


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: 1557
Number of extensions: 76
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: 814
Length adjustment: 41
Effective length of query: 774
Effective length of database: 773
Effective search space:   598302
Effective search space used:   598302
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:

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