GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cimA in Desulfovibrio vulgaris Hildenborough

Align (R)-citramalate synthase (EC 2.3.1.182) (characterized)
to candidate 207383 DVU1914 2-isopropylmalate synthase/homocitrate synthase family protein

Query= BRENDA::Q74C76
         (528 letters)



>lcl|MicrobesOnline__882:207383 DVU1914 2-isopropylmalate
           synthase/homocitrate synthase family protein
          Length = 538

 Score =  576 bits (1484), Expect = e-169
 Identities = 292/529 (55%), Positives = 382/529 (72%), Gaps = 8/529 (1%)

Query: 4   VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE 63
           + LYDTTLRDG+Q+EDI+    DK++IA +LDE+GI YIEGGWPGSNP DVAFFK+I+  
Sbjct: 5   IHLYDTTLRDGSQSEDINLNTPDKLKIALRLDELGIAYIEGGWPGSNPVDVAFFKEIRNY 64

Query: 64  KLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENL 123
            L QAKI+AFGST     T + D NLK +  A  D   IFGK+ + H  EALR+    NL
Sbjct: 65  NLKQAKISAFGSTHHPSHTAENDPNLKAIAAARTDAAAIFGKSCERHAREALRLDGRRNL 124

Query: 124 ELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTM 183
           ++I DS+ +LK  V EVF+DAEHFFDGY+ N  YA++ L+ A +A  D +VLCDTNGGT+
Sbjct: 125 DIIHDSIAFLKKQVAEVFFDAEHFFDGYRHNAAYALEVLRRAHEAGGDVLVLCDTNGGTL 184

Query: 184 PFELVEIIREVRKHI-TAPLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGNA 242
           P E+ +I+  VR+ +  A LGIH HND E AVANS+ AV  G VQVQGT+NG GERCGNA
Sbjct: 185 PHEVHDIVTAVREQLPEAKLGIHAHNDCEVAVANSIAAVQAGAVQVQGTMNGVGERCGNA 244

Query: 243 NLCSIIPALKLKM--KRECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKGG 300
           NL S+IP L+LK      C+ + +L++L  +S +V E+ NL P   Q +VG SAFAHKGG
Sbjct: 245 NLSSVIPILELKSAGAYACLPEGRLQQLTAVSSYVSEVTNLPPFSRQPFVGRSAFAHKGG 304

Query: 301 VHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEIL 360
           VHVSA+ R+   YEH+ PE VGN  RVL+++L+GRSNI++ A  F   +D  +PV   ++
Sbjct: 305 VHVSAVNRNATLYEHITPESVGNHQRVLITELAGRSNIVSLARRFGFHLDKDEPVVKGLM 364

Query: 361 ENIKEMENRGYQFEGAEASFELLMKRALGTH--RKFFSVIGFRVIDEKRHEDQKPLSEAT 418
             +K+  + GY +  AEAS ELL+ R L     R+FF +I FRV++ K+  D +P+SEA+
Sbjct: 365 NELKKKASLGYDYAAAEASVELLLLRKLARRGVREFFKLIQFRVLESKQENDLEPMSEAS 424

Query: 419 IMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQ---GT 475
           +MV+V G IEHTAA G GPVNALDNALRKAL  FYPR++E++LLD+KVRVL   +   GT
Sbjct: 425 VMVEVEGIIEHTAATGRGPVNALDNALRKALSSFYPRIREMRLLDFKVRVLTGTETDGGT 484

Query: 476 ASSIRVLIESGDKESRWGTVGVSENIVDASYQALLDSVEYKLHKSEEIE 524
           AS++RVLIESGD +SRW TVGVS NI++AS+QAL DS+ YKL+K E ++
Sbjct: 485 ASTVRVLIESGDADSRWVTVGVSYNIIEASWQALADSMTYKLYKDEHVQ 533


Lambda     K      H
   0.317    0.135    0.387 

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: 778
Number of extensions: 33
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: 528
Length of database: 538
Length adjustment: 35
Effective length of query: 493
Effective length of database: 503
Effective search space:   247979
Effective search space used:   247979
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate 207383 DVU1914 (2-isopropylmalate synthase/homocitrate synthase family protein)
to HMM TIGR00977 (cimA: citramalate synthase (EC 2.3.1.182))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00977.hmm
# target sequence database:        /tmp/gapView.9096.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00977  [M=526]
Accession:   TIGR00977
Description: citramal_synth: citramalate synthase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   9.7e-212  689.8   0.1   1.1e-211  689.5   0.1    1.0  1  lcl|MicrobesOnline__882:207383  DVU1914 2-isopropylmalate syntha


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207383  DVU1914 2-isopropylmalate synthase/homocitrate synthase family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.5   0.1  1.1e-211  1.1e-211       2     522 ..       5     531 ..       4     535 .. 0.97

  Alignments for each domain:
  == domain 1  score: 689.5 bits;  conditional E-value: 1.1e-211
                       TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsstrrpdkk 80 
                                     ++lydttlrdG+q e + l   dk++ia +ld+lGi yieGGwpg+np dvaff+++++ nlk+ak++af+st  p + 
  lcl|MicrobesOnline__882:207383   5 IHLYDTTLRDGSQSEDINLNTPDKLKIALRLDELGIAYIEGGWPGSNPVDVAFFKEIRNYNLKQAKISAFGSTHHPSHT 83 
                                     89***************************************************************************** PP

                       TIGR00977  81 veedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffdGykanpeyalkt 159
                                      e+d++l+a+  a t   +ifGks + h  eal+     nl++i+d++++lk+++ ev +daehffdGy+ n  yal++
  lcl|MicrobesOnline__882:207383  84 AENDPNLKAIAAARTDAAAIFGKSCERHAREALRLDGRRNLDIIHDSIAFLKKQVAEVFFDAEHFFDGYRHNAAYALEV 162
                                     ******************************************************************************* PP

                       TIGR00977 160 lkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahndsetavansllaveaGavqvqGtinGlGerc 238
                                     l+ a++aG d+lvl+dtnGGtlphe+++i++ v+++l +++lGihahnd e+avans++av+aGavqvqGt+nG+Gerc
  lcl|MicrobesOnline__882:207383 163 LRRAHEAGGDVLVLCDTNGGTLPHEVHDIVTAVREQLPEAKLGIHAHNDCEVAVANSIAAVQAGAVQVQGTMNGVGERC 241
                                     ******************************************************************************* PP

                       TIGR00977 239 Gnanlcslipnlqlkl..gldviekenlkkltevarlvaeivnlaldenmpyvGesafahkGGvhvsavkrnpktyehi 315
                                     Gnanl s+ip l lk    + ++++ +l++lt v+ +v+e++nl++ ++ p+vG+safahkGGvhvsav+rn++ yehi
  lcl|MicrobesOnline__882:207383 242 GNANLSSVIPILELKSagAYACLPEGRLQQLTAVSSYVSEVTNLPPFSRQPFVGRSAFAHKGGVHVSAVNRNATLYEHI 320
                                     ***************74359*********************************************************** PP

                       TIGR00977 316 dpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkr..kk 392
                                      pe vGn++++ ++elaG+sn+++ ++ +G+++d+++p v+ +++++k+    Gy++ aaeas+ell+ ++l +r  ++
  lcl|MicrobesOnline__882:207383 321 TPESVGNHQRVLITELAGRSNIVSLARRFGFHLDKDEPVVKGLMNELKKKASLGYDYAAAEASVELLLLRKLARRgvRE 399
                                     ********************************************************************99998754489 PP

                       TIGR00977 393 yfevdgfrvliakrrdeeslseaeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilne 471
                                     +f++  frvl  k+ ++   + +ea v v veg  e+taa G Gpv+ald+alrkal  fyp++++++l+d+kvr+l +
  lcl|MicrobesOnline__882:207383 400 FFKLIQFRVLESKQEND-LEPMSEASVMVEVEGIIEHTAATGRGPVNALDNALRKALSSFYPRIREMRLLDFKVRVLTG 477
                                     **********9998887.6788999999************************************************975 PP

                       TIGR00977 472 ...saGtsaktrvliessdGkrrwgtvGvseniieasytallesieyklrkdee 522
                                        + Gt +++rvlies d + rw tvGvs niieas++al +s+ ykl kde 
  lcl|MicrobesOnline__882:207383 478 tetDGGTASTVRVLIESGDADSRWVTVGVSYNIIEASWQALADSMTYKLYKDEH 531
                                     222679*********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (538 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.34
//
[ok]

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the 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