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_055435097.1 ASC41_RS02630 bifunctional aspartate kinase/homoserine dehydrogenase I

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



>NCBI__GCF_001418085.1:WP_055435097.1
          Length = 1131

 Score =  472 bits (1214), Expect = e-137
 Identities = 294/826 (35%), Positives = 480/826 (58%), Gaps = 42/826 (5%)

Query: 1    MKIIKFGGSSIANYENIQKVFSIIEQKSE-KEAFALVFSAFGGVTEQLLQCANIAQQSEE 59
            MKI+KFGG S+AN E + +V SIIE K + +E  A+V SA G  T+QL      A + +E
Sbjct: 327  MKILKFGGKSLANGEGLNRVISIIENKVKAEENIAVVVSARGKATDQLESILEKAVK-DE 385

Query: 60   SYHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDY 119
            +Y T     +              Q+ T +   +  F  L  LF G+ L+ + S +  D 
Sbjct: 386  AYATDFDAFKN------------DQKGTIVVDFETEFLRLESLFAGVQLLGDYSPKIKDE 433

Query: 120  VLSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSH 179
            VL+ GE +S  ++   L  K I     DAR  +KTDD FG+AK     + K +  +FK +
Sbjct: 434  VLAQGELISAKLITGLLVDKNINAKVADARTFIKTDDTFGNAKPIDALSKKNVVAYFKQN 493

Query: 180  DD--IKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRL 237
            +   + ++TGFI S    +TTT+GR+GS+YTA++ A  L AE+++ +T V+G+ TA+P L
Sbjct: 494  NGTTVNIVTGFIASNRDNKTTTLGRNGSNYTAALLANYLDAEELQNYTHVNGIYTANPDL 553

Query: 238  VYTAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDS 297
            V  A  I +LS+ EA EL++FG  ++   T+ P ++++IP+ I NTF P++ GT I+  +
Sbjct: 554  VADAIKIERLSFTEANELANFGTTILHAKTIIPLIEKNIPLRILNTFNPEDKGTIITAQN 613

Query: 298  GEGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICV 357
             + K I+ +S +DN++++N++G GL+  VGV  R F  L+   I++ +ISQ SSE  I +
Sbjct: 614  -KDKGIRSLSVLDNVALVNIEGRGLLGKVGVDARIFTALSKENISVSIISQGSSERGIGL 672

Query: 358  AIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQ--HNPGASGRMFQ 415
             I ++ A+RA  V+E+EF  +  S ++++I ++ D++VI+++G+ +   H P      F 
Sbjct: 673  VIEAEHANRAVIVLEQEFENDFYSQDINKISVIDDVSVISIIGQELSTFHKP------FN 726

Query: 416  ALGRNNVNVAAIAQGSSELNISAVITQADLQKALNALH-EAFFLSDYKVLHLFLVGVGLI 474
             L +N +         +  N+S V+ + +L KA+N +H E F +S  K ++L + G GL+
Sbjct: 727  NLIKNQIIPILFNNTITGENVSIVVKKKELHKAVNVIHGEIFGIS--KKINLAIFGHGLV 784

Query: 475  GKALTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDK 534
            G AL   I    K++++   + + I  +ANS+   F ++G D       + N E   ++ 
Sbjct: 785  GGALVNQIIASAKDIEKRKGIKLNIFAIANSQKALFSKNGIDENWKNTLETNGENYKIED 844

Query: 535  FIGTMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLA 594
                  + +  N + +D T+S +    Y ++++    +V+ NK AN+  LE Y +L+   
Sbjct: 845  VFQFAKDNHLENLIAIDNTSSLEFVSNYIKLVEQGFDLVSSNKIANTIDLEFYNELRNTL 904

Query: 595  GQRGVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSEL-EKGMPFSE 653
             +    + YETNV AGLP+I+T++ L LSG+++ RI  V SGS++Y+F+    +   F+ 
Sbjct: 905  EKHQKSYLYETNVGAGLPLIDTIKLLHLSGENIVRIRGVFSGSLSYLFNTFSSEDTSFAT 964

Query: 654  VVAQAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFE--DVEIQSMVPEDCEDAA 711
            V+ QA +KG+TEP+PR+DLSG DVARK+LIL RE   DLH E  DV I++++PE   +  
Sbjct: 965  VLQQALDKGFTEPNPREDLSGNDVARKLLILAREL--DLHNEIGDVTIENLIPEPLRE-I 1021

Query: 712  SVPEFFKKLQKHDGHFQQLLDEANAKGEKLRFMATL------ENG-KAKVGLNSLDSEHP 764
               +F   L + +  FQ+ + EA  +G  LR++  L      ENG +  V L S+ S+ P
Sbjct: 1022 ETSQFLDSLDEMNTVFQK-IKEAQKEGHVLRYIGDLHGDLSQENGAQLDVKLESVPSQSP 1080

Query: 765  FFTLKGSDNMILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRL 810
               L+G+D++    TE Y + P++++G GAGA VTA GVF DI+RL
Sbjct: 1081 LGALQGADSIFEIYTESYGEKPIVIQGAGAGASVTARGVFGDILRL 1126


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: 2042
Number of extensions: 96
Number of successful extensions: 12
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: 1131
Length adjustment: 44
Effective length of query: 771
Effective length of database: 1087
Effective search space:   838077
Effective search space used:   838077
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: 57 (26.6 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