GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Echinicola vietnamensis KMM 6221, DSM 17526

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate Echvi_2459 Echvi_2459 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>FitnessBrowser__Cola:Echvi_2459
          Length = 429

 Score =  405 bits (1040), Expect = e-117
 Identities = 216/421 (51%), Positives = 287/421 (68%), Gaps = 7/421 (1%)

Query: 371 QKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFE 430
           QK L+RP+QK  +I  +V PI+  V  +G+ AL ++  ++D V++ N +++     E +E
Sbjct: 13  QKELARPVQKMKDIQKIVKPIMRKVSRQGDKALKKFALEYDHVEIDNLLVSRDEINEAYE 72

Query: 431 GLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAI 490
            + E +K A+  +  N+ KFH AQ  TE L +E   GV C R   PI+KVGLYIPGGTA 
Sbjct: 73  QVDESLKSAIQQAKVNIEKFHKAQ-QTEDLSMEVMEGVTCMRRSVPIQKVGLYIPGGTAP 131

Query: 491 LPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAA 550
           L ST LMLG+PA +A C+EIV  +PP K +GK+ P ++Y A  +G  KIV AGGAQA+AA
Sbjct: 132 LFSTVLMLGIPANIAGCEEIVLCTPPNK-EGKIHPAILYTANLIGIDKIVKAGGAQAIAA 190

Query: 551 MAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDF 610
           + YGTE++P+V KI GPGNQ+VTAAK   Q  T+   +IDMPAGPSEVLV ADE A   F
Sbjct: 191 LTYGTESVPQVAKIFGPGNQYVTAAK---QLATKKGIAIDMPAGPSEVLVYADESAVPAF 247

Query: 611 VASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIVL 670
           VA+DLLSQAEHGIDSQVILV    + K  ++    V  Q  +LPR DI +K + +S  V+
Sbjct: 248 VAADLLSQAEHGIDSQVILVAT--ASKVAKKTLKEVDKQLAKLPRKDIAKKALENSIAVV 305

Query: 671 CDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTL 730
               E+A+ + N YAPEHLI+ +AN ++ V  + NAGSVF+G +TPES GDY+SGTNHTL
Sbjct: 306 MGNQEKAIALINDYAPEHLIINVANEDEVVANIVNAGSVFIGNFTPESAGDYASGTNHTL 365

Query: 731 PTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSK 790
           PTYG+AR YSG +  +F K IT Q IT +GL+N+G  +  +A  E LD H+NAV IR+  
Sbjct: 366 PTYGFARNYSGVSLDSFVKKITYQKITEKGLQNLGPTIEVMAGNELLDAHKNAVSIRLKY 425

Query: 791 L 791
           L
Sbjct: 426 L 426


Lambda     K      H
   0.315    0.133    0.371 

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: 793
Number of extensions: 36
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: 799
Length of database: 429
Length adjustment: 36
Effective length of query: 763
Effective length of database: 393
Effective search space:   299859
Effective search space used:   299859
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: 42 (22.0 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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