Alignments for a candidate for cimA in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Azospirillum brasilense Sp245

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate AZOBR_RS04265 AZOBR_RS04265 2-isopropylmalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>FitnessBrowser__azobra:AZOBR_RS04265
          Length = 534

 Score =  508 bits (1307), Expect = e-148
 Identities = 272/524 (51%), Positives = 350/524 (66%), Gaps = 10/524 (1%)

Query: 4   VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE 63
           + LYDTTLRDG Q +D+ F V DKI IA  LD +GI Y+EGGWPG+NP D  FF +    
Sbjct: 6   IYLYDTTLRDGAQTQDVDFSVADKIAIARDLDRLGIDYVEGGWPGANPTDDQFFAEAPD- 64

Query: 64  KLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENL 123
            L+++   AFG TRR   +   D  L  LIQ++     I GKTWDFHV  AL I  EEN+
Sbjct: 65  -LARSTFTAFGMTRRPGRSTANDPQLAALIQSKARAVCIVGKTWDFHVDVALAIPREENI 123

Query: 124 ELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTM 183
           ELI DS+  LKA   E  +DAEHFFDGYK NP YA   +KAA +A A  +VLCDTNGGT+
Sbjct: 124 ELIADSIAALKAAKGEALFDAEHFFDGYKRNPAYAASCIKAAYEAGARWVVLCDTNGGTL 183

Query: 184 PFELVEIIREVRKHITAP---LGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCG 240
           P E+ EI+R+V      P   LGIH HND+E AVANSL AV  G+  VQGTING GERCG
Sbjct: 184 PHEIDEIVRQVIDEHGIPGDRLGIHCHNDTENAVANSLAAVRAGVRMVQGTINGLGERCG 243

Query: 241 NANLCSIIPALKLKMKREC-IGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKG 299
           NANL S+IP+L LKM  +  I    L  L ++SR   E  N +PN+H  YVG SAFAHKG
Sbjct: 244 NANLVSLIPSLMLKMGCDVGIKPADLPLLTEISRKFDERLNRAPNRHAPYVGASAFAHKG 303

Query: 300 GVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEI 359
           G+HVSA+++ P +YEH+ PE VGN  ++++SD +GRSN++A+  E  + +D KD     +
Sbjct: 304 GLHVSAVEKDPSSYEHVEPEAVGNRRQIVMSDQAGRSNVIARLREMGMAVDPKDERLNRL 363

Query: 360 LENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHEDQKPL---SE 416
           L+ +K+ +  GY ++ AEASFELL++R LG    +F++  F V DE+R+  +  L   SE
Sbjct: 364 LDIVKQRDTEGYAYDTAEASFELLVRRELGEVPDYFTLKRFHVTDERRYNAKGELVVESE 423

Query: 417 ATIMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGTA 476
           A + VK+GGK  H  A GNGPVNALD A+RKALE  YP L  VKL DY+VR+L A  GT 
Sbjct: 424 AVVRVKIGGKEYHEVASGNGPVNALDTAMRKALEPLYPLLDGVKLSDYRVRILAAKDGTG 483

Query: 477 SSIRVLIESGDKESR-WGTVGVSENIVDASYQALLDSVEYKLHK 519
           +  RVLI S + + + W T+GVS NI++AS +AL+DS  +KL K
Sbjct: 484 AMPRVLIRSRNGDGQEWSTLGVSTNIIEASMEALVDSYTFKLFK 527


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: 689
Number of extensions: 24
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: 534
Length adjustment: 35
Effective length of query: 493
Effective length of database: 499
Effective search space:   246007
Effective search space used:   246007
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 AZOBR_RS04265 AZOBR_RS04265 (2-isopropylmalate 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.3680.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-204  666.6   0.0   1.3e-204  666.3   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS04265  AZOBR_RS04265 2-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS04265  AZOBR_RS04265 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  666.3   0.0  1.3e-204  1.3e-204       2     519 ..       6     527 ..       5     532 .. 0.97

  Alignments for each domain:
  == domain 1  score: 666.3 bits;  conditional E-value: 1.3e-204
                                 TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvva 70 
                                               ++lydttlrdGaq++ v +s+ dki ia+ ld lGi+y+eGGwpganp d +ff ++   +l +   +a
  lcl|FitnessBrowser__azobra:AZOBR_RS04265   6 IYLYDTTLRDGAQTQDVDFSVADKIAIARDLDRLGIDYVEGGWPGANPTDDQFFAEAP--DLARSTFTA 72 
                                               89****************************************************9875..688999*** PP

                                 TIGR00977  71 fsstrrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadevi 139
                                               f+ trrp +   +d+ql ali+++++ v i Gk+wd+hv  al    een+++i d+++ lk    e +
  lcl|FitnessBrowser__azobra:AZOBR_RS04265  73 FGMTRRPGRSTANDPQLAALIQSKARAVCIVGKTWDFHVDVALAIPREENIELIADSIAALKAAKGEAL 141
                                               ********************************************************************* PP

                                 TIGR00977 140 ydaehffdGykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrl..kdpqlGihah 206
                                               +daehffdGyk np ya   +k+a +aGa w+vl+dtnGGtlphei+ei+++v  +      +lGih h
  lcl|FitnessBrowser__azobra:AZOBR_RS04265 142 FDAEHFFDGYKRNPAYAASCIKAAYEAGARWVVLCDTNGGTLPHEIDEIVRQVIDEHgiPGDRLGIHCH 210
                                               ****************************************************97665336778****** PP

                                 TIGR00977 207 ndsetavansllaveaGavqvqGtinGlGercGnanlcslipnlqlklgldv.iekenlkkltevarlv 274
                                               nd+e avansl+av+aG ++vqGtinGlGercGnanl slip l+lk+g dv i++ +l  lte++r  
  lcl|FitnessBrowser__azobra:AZOBR_RS04265 211 NDTENAVANSLAAVRAGVRMVQGTINGLGERCGNANLVSLIPSLMLKMGCDVgIKPADLPLLTEISRKF 279
                                               ***************************************************9899************** PP

                                 TIGR00977 275 aeivnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklke 343
                                                e  n+a+++++pyvG safahkGG+hvsav+++p +yeh++pe vGn+r+iv+s++aG+snv+ +l+e
  lcl|FitnessBrowser__azobra:AZOBR_RS04265 280 DERLNRAPNRHAPYVGASAFAHKGGLHVSAVEKDPSSYEHVEPEAVGNRRQIVMSDQAGRSNVIARLRE 348
                                               ********************************************************************* PP

                                 TIGR00977 344 lGieidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdee.. 410
                                               +G+++d+k+ +++++l+ +k+ + +Gy +++aeas+ellvr+ lG++ +yf ++ f+v+ ++r +++  
  lcl|FitnessBrowser__azobra:AZOBR_RS04265 349 MGMAVDPKDERLNRLLDIVKQRDTEGYAYDTAEASFELLVRRELGEVPDYFTLKRFHVTDERRYNAKge 417
                                               **********************************************************99988776543 PP

                                 TIGR00977 411 slseaeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsakt 479
                                                + e+ea vrv + g+e +++a GnGpv+ald a+rkale +yp l  +kl dy+vril  + Gt a  
  lcl|FitnessBrowser__azobra:AZOBR_RS04265 418 LVVESEAVVRVKIGGKEYHEVASGNGPVNALDTAMRKALEPLYPLLDGVKLSDYRVRILAAKDGTGAMP 486
                                               899****************************************************************** PP

                                 TIGR00977 480 rvliessdGk.rrwgtvGvseniieasytallesieyklrk 519
                                               rvli s +G+ + w+t+Gvs niieas  al++s  +kl k
  lcl|FitnessBrowser__azobra:AZOBR_RS04265 487 RVLIRSRNGDgQEWSTLGVSTNIIEASMEALVDSYTFKLFK 527
                                               *********9457*************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (534 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.89
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis