GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Azorhizobium caulinodans ORS 571

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_012170314.1 AZC_RS09265 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_000010525.1:WP_012170314.1
          Length = 537

 Score =  439 bits (1130), Expect = e-128
 Identities = 242/525 (46%), Positives = 331/525 (63%), Gaps = 15/525 (2%)

Query: 6   LYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKEKL 65
           L+DTTLRDG Q   + F + DK+ +   L+ +G+ Y+E G+PG+NP D   F    +++ 
Sbjct: 14  LFDTTLRDGAQTNGVDFTLADKLNVIGLLNRLGVDYVEAGYPGANPTDTQLFA---QKRP 70

Query: 66  SQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENLEL 125
           S A++ AFG T+RA  +   D  +  L+ AE D      K   F V  AL  + EENL  
Sbjct: 71  SAARVTAFGMTKRAGRSVSNDPGVAALLAAEADAICFVAKASAFQVRVALETTEEENLAS 130

Query: 126 IFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTMPF 185
           I +S+    A   E   D EHFFDG+K NPD+A+   +AA  A A  +VLCDTNGGT+P 
Sbjct: 131 IRESVAAAVAAGREALVDCEHFFDGFKENPDFALACAEAAYQAGARWVVLCDTNGGTLPH 190

Query: 186 ELVEIIREVRKHITAP-LGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGNANL 244
           E+  I+  V   +    +GIH HND+E AVANSL AV  G  Q+QGT+NG GERCGNANL
Sbjct: 191 EVEAIVARVTARVPGSHVGIHAHNDTEQAVANSLAAVRAGARQIQGTLNGLGERCGNANL 250

Query: 245 CSIIPALKLKMK-----RECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKG 299
           CS+IP L LK          +  + L ++  +SR + E+ N SP++H  YVG SAFA K 
Sbjct: 251 CSLIPTLLLKGDYAERFETGVSREALAEIGVVSRTLDEMLNRSPDRHAPYVGESAFATKA 310

Query: 300 GVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEI 359
           G+H SAI + P TYEH+ PE VGN  RVLVSD +GRSN+LA+ E   + +D  DP    +
Sbjct: 311 GIHASAILKDPATYEHVPPEAVGNQRRVLVSDQAGRSNVLAELERLGVPVDRADPRLARL 370

Query: 360 LENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHE---DQKPLSE 416
           L+ +KE E  GY +E A+ASF LL +R L +   FF+V  F V  E+R+    +   ++E
Sbjct: 371 LDEVKEREALGYAYEAADASFALLARRMLHSVPDFFTVERFSVKVERRYNAKGEMTTVAE 430

Query: 417 ATIMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGTA 476
           A + V+VG ++  +AAEGNGPVNALD ALRK L K+ P +  ++L DY+VR+L    GT 
Sbjct: 431 AIVKVRVGDEVFISAAEGNGPVNALDVALRKDLGKYQPYIAGLRLTDYRVRIL--NGGTE 488

Query: 477 SSIRVLIESGDKE-SRWGTVGVSENIVDASYQALLDSVEYKLHKS 520
           +  RVL+ES D+  +RW TVGVS NI+DAS++ALLDS+ ++L +S
Sbjct: 489 AVTRVLVESTDESGARWTTVGVSPNIIDASFEALLDSITWQLLRS 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: 628
Number of extensions: 25
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_012170314.1 AZC_RS09265 (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.3351179.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     5e-186  604.9   0.0   6.1e-186  604.6   0.0    1.0  1  NCBI__GCF_000010525.1:WP_012170314.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010525.1:WP_012170314.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  604.6   0.0  6.1e-186  6.1e-186       2     519 ..      12     532 ..      11     535 .. 0.95

  Alignments for each domain:
  == domain 1  score: 604.6 bits;  conditional E-value: 6.1e-186
                             TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsst 74 
                                           l+l+dttlrdGaq++Gv ++l dk+++   l+ lG++y+e G+pganp d+++f + +      a+v+af+ t
  NCBI__GCF_000010525.1:WP_012170314.1  12 LYLFDTTLRDGAQTNGVDFTLADKLNVIGLLNRLGVDYVEAGYPGANPTDTQLFAQKRP---SAARVTAFGMT 81 
                                           89****************************************************98665...5799******* PP

                             TIGR00977  75 rrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffd 147
                                           +r  + v++d+ + al+ ae+  +    k+  + v  al+tt eenl+ i ++v+     ++e + d ehffd
  NCBI__GCF_000010525.1:WP_012170314.1  82 KRAGRSVSNDPGVAALLAAEADAICFVAKASAFQVRVALETTEEENLASIRESVAAAVAAGREALVDCEHFFD 154
                                           ************************************************************************* PP

                             TIGR00977 148 GykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahndsetavansllav 220
                                           G+k np++al+  ++a +aGa w+vl+dtnGGtlphe+e i+ +v  r+  +++Gihahnd+e avansl+av
  NCBI__GCF_000010525.1:WP_012170314.1 155 GFKENPDFALACAEAAYQAGARWVVLCDTNGGTLPHEVEAIVARVTARVPGSHVGIHAHNDTEQAVANSLAAV 227
                                           ************************************************************************* PP

                             TIGR00977 221 eaGavqvqGtinGlGercGnanlcslipnlqlklgl.....dviekenlkkltevarlvaeivnlaldenmpy 288
                                           +aGa+q+qGt+nGlGercGnanlcslip l lk ++       + +e l+++  v+r + e+ n+++d+++py
  NCBI__GCF_000010525.1:WP_012170314.1 228 RAGARQIQGTLNGLGERCGNANLCSLIPTLLLKGDYaerfeTGVSREALAEIGVVSRTLDEMLNRSPDRHAPY 300
                                           **********************************994333225899*************************** PP

                             TIGR00977 289 vGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkk 361
                                           vGesafa k G+h+sa+ ++p tyeh+ pe vGn+r++ vs++aG+snvl  l+ lG+ +d+ +p++ ++l++
  NCBI__GCF_000010525.1:WP_012170314.1 301 VGESAFATKAGIHASAILKDPATYEHVPPEAVGNQRRVLVSDQAGRSNVLAELERLGVPVDRADPRLARLLDE 373
                                           ************************************************************************* PP

                             TIGR00977 362 ikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdee....slseaeatvrvsvegaeelt 430
                                           +ke e+ Gy +eaa+as+ ll r++l ++ ++f v+ f v++++r +++    +++ea ++vrv +e      
  NCBI__GCF_000010525.1:WP_012170314.1 374 VKEREALGYAYEAADASFALLARRMLHSVPDFFTVERFSVKVERRYNAKgemtTVAEAIVKVRVGDE--VFIS 444
                                           *******************************************998876544444555555555555..5689 PP

                             TIGR00977 431 aaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsaktrvliessdGk.rrwgtvGvsenii 502
                                           aaeGnGpv+ald alrk l k+ p ++ l+ltdy+vriln+  Gt+a trvl+es+d    rw+tvGvs+nii
  NCBI__GCF_000010525.1:WP_012170314.1 445 AAEGNGPVNALDVALRKDLGKYQPYIAGLRLTDYRVRILNG--GTEAVTRVLVESTDESgARWTTVGVSPNII 515
                                           ***************************************97..9************965379*********** PP

                             TIGR00977 503 easytallesieyklrk 519
                                           +as+ all+si ++l +
  NCBI__GCF_000010525.1:WP_012170314.1 516 DASFEALLDSITWQLLR 532
                                           ************99865 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 13.80
//
[ok]

This GapMind analysis is from Jul 25 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