GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Phyllobacterium brassicacearum STM 196

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_106712020.1 CU102_RS15545 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_003010955.1:WP_106712020.1
          Length = 537

 Score =  474 bits (1221), Expect = e-138
 Identities = 265/532 (49%), Positives = 343/532 (64%), Gaps = 15/532 (2%)

Query: 4   VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE 63
           + L+DTTLRDG Q   I F VEDK  IA  LDE G  Y+EGG+PG+NP D AFF +   +
Sbjct: 6   IYLFDTTLRDGQQTPGIDFSVEDKKVIADMLDEFGFDYVEGGYPGANPTDTAFFAE---K 62

Query: 64  KLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENL 123
           +  +AK AAFG T+RA V+   D  L  LI++  D     GK+WD+HV  AL  + EENL
Sbjct: 63  RTKRAKFAAFGMTKRAGVSASNDPGLAGLIRSSADTVCFVGKSWDYHVRVALSCTNEENL 122

Query: 124 ELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTM 183
           E I  S++       E   D EHFFDGYKANPDYA+   K A DA A  IVLCDTNGG+ 
Sbjct: 123 ESIDASVKAAIEAGKEAIVDCEHFFDGYKANPDYALACAKTAYDAGARWIVLCDTNGGSQ 182

Query: 184 PFELVEIIREVRKHITAP-LGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGNA 242
           P E+ EI+R+V K I    LGIH HND+E AVANSL A+  G+  VQGT+NG GERCGNA
Sbjct: 183 PAEVAEIVRKVTKLIPGDHLGIHAHNDTEQAVANSLAAIDAGVRHVQGTLNGIGERCGNA 242

Query: 243 NLCSIIPALKLKMK-----RECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAH 297
           NL +IIP L LK          I  ++L+ L  LSR   EL N +PN   A+VG SAFA 
Sbjct: 243 NLVTIIPTLMLKPAWSDRFETGISLEKLQGLARLSRSFDELLNRAPNPQGAFVGTSAFAT 302

Query: 298 KGGVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTL 357
           K G+H SA+ + P TYEH+ PE VGN  +V+VSD  G+SN + + E   I +   DP   
Sbjct: 303 KAGIHASALIKEPATYEHVPPETVGNRRKVMVSDQGGKSNFINELERRGIPVAKSDPRLD 362

Query: 358 EILENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHE---DQKPL 414
            ++  +KE E  GY +EGA+ASFELL +R LGT  +FF V  FR + E+R +   + K +
Sbjct: 363 TLIALVKEHEAEGYAYEGADASFELLARRTLGTVPEFFKVDSFRCMVERRFDANGNIKTV 422

Query: 415 SEATIMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQG 474
           SEA + V++ G+   + AEG+GPVNALD ALRK + ++   + ++ L D+KVR+L    G
Sbjct: 423 SEAVVRVEIDGETRMSVAEGHGPVNALDLALRKDMGRYQHEIDDLVLADFKVRIL--NGG 480

Query: 475 TASSIRVLIESGD-KESRWGTVGVSENIVDASYQALLDSVEYKLHKSEEIEG 525
           T +  RVLIES D   +RW TVGVS+NI+DAS+QAL+DSV YKL K+ ++ G
Sbjct: 481 TEAITRVLIESTDSSNARWWTVGVSDNIIDASFQALMDSVVYKLMKNRDLAG 532


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: 728
Number of extensions: 28
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: 528
Length of database: 537
Length adjustment: 35
Effective length of query: 493
Effective length of database: 502
Effective search space:   247486
Effective search space used:   247486
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 WP_106712020.1 CU102_RS15545 (citramalate synthase)
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.1804797.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.7e-186  605.4   0.0   4.5e-186  605.1   0.0    1.0  1  NCBI__GCF_003010955.1:WP_106712020.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106712020.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  605.1   0.0  4.5e-186  4.5e-186       2     521 ..       6     528 ..       5     532 .. 0.96

  Alignments for each domain:
  == domain 1  score: 605.1 bits;  conditional E-value: 4.5e-186
                             TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsst 74 
                                           ++l+dttlrdG q+ G+ +s+edk  ia+ ld++G +y+eGG+pganp d+aff +      k+ak +af+ t
  NCBI__GCF_003010955.1:WP_106712020.1   6 IYLFDTTLRDGQQTPGIDFSVEDKKVIADMLDEFGFDYVEGGYPGANPTDTAFFAEK---RTKRAKFAAFGMT 75 
                                           89****************************************************865...5689********* PP

                             TIGR00977  75 rrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffd 147
                                           +r  +  ++d+ l  li++ +  v   Gkswd hv  al  t eenl+ i  +v+   + ++e i d ehffd
  NCBI__GCF_003010955.1:WP_106712020.1  76 KRAGVSASNDPGLAGLIRSSADTVCFVGKSWDYHVRVALSCTNEENLESIDASVKAAIEAGKEAIVDCEHFFD 148
                                           ************************************************************************* PP

                             TIGR00977 148 GykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahndsetavansllav 220
                                           Gykanp+yal+  k+a +aGa w+vl+dtnGG+ p e+ ei++kv k +   +lGihahnd+e avansl+a+
  NCBI__GCF_003010955.1:WP_106712020.1 149 GYKANPDYALACAKTAYDAGARWIVLCDTNGGSQPAEVAEIVRKVTKLIPGDHLGIHAHNDTEQAVANSLAAI 221
                                           ************************************************************************* PP

                             TIGR00977 221 eaGavqvqGtinGlGercGnanlcslipnlqlklgl....d.viekenlkkltevarlvaeivnlaldenmpy 288
                                            aG ++vqGt+nG+GercGnanl ++ip l+lk  +    +  i  e+l+ l  ++r   e+ n+a++ +  +
  NCBI__GCF_003010955.1:WP_106712020.1 222 DAGVRHVQGTLNGIGERCGNANLVTIIPTLMLKPAWsdrfEtGISLEKLQGLARLSRSFDELLNRAPNPQGAF 294
                                           *********************************8752222335999*************************** PP

                             TIGR00977 289 vGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkk 361
                                           vG safa k G+h+sa+ ++p tyeh+ pe vGn+rk++vs++ Gksn ++ l+  Gi + +++p++ ++++ 
  NCBI__GCF_003010955.1:WP_106712020.1 295 VGTSAFATKAGIHASALIKEPATYEHVPPETVGNRRKVMVSDQGGKSNFINELERRGIPVAKSDPRLDTLIAL 367
                                           ************************************************************************* PP

                             TIGR00977 362 ikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdee..slseaeatvrvsvegaeeltaa 432
                                           +ke e++Gy +e+a+as+ell r++lG++ ++f+vd+fr ++++r d++    + +ea vrv ++g   + +a
  NCBI__GCF_003010955.1:WP_106712020.1 368 VKEHEAEGYAYEGADASFELLARRTLGTVPEFFKVDSFRCMVERRFDANgnIKTVSEAVVRVEIDGETRMSVA 440
                                           ***********************************************99633455899*************** PP

                             TIGR00977 433 eGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsaktrvliessdG.krrwgtvGvseniiea 504
                                           eG+Gpv+ald alrk + ++  ++ dl l d+kvriln+  Gt+a trvlies+d  + rw tvGvs+nii+a
  NCBI__GCF_003010955.1:WP_106712020.1 441 EGHGPVNALDLALRKDMGRYQHEIDDLVLADFKVRILNG--GTEAITRVLIESTDSsNARWWTVGVSDNIIDA 511
                                           *************************************97..9************97367************** PP

                             TIGR00977 505 sytallesieyklrkde 521
                                           s++al++s++ykl+k+ 
  NCBI__GCF_003010955.1:WP_106712020.1 512 SFQALMDSVVYKLMKNR 528
                                           **************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (537 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 29.58
//
[ok]

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