GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcB in Cupriavidus basilensis 4G11

Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate RR42_RS12175 RR42_RS12175 malate synthase

Query= reanno::BFirm:BPHYT_RS12305
         (536 letters)



>FitnessBrowser__Cup4G11:RR42_RS12175
          Length = 528

 Score =  838 bits (2165), Expect = 0.0
 Identities = 403/527 (76%), Positives = 455/527 (86%)

Query: 10  SLQLPQGMEITAEIKPGYDAILSREALELVAALHRTFEPRRQQLLQARAERTKRLDAGER 69
           ++ LP GM+IT EI P Y+ IL+  AL LV  LHR FEPRRQ+LL AR ERTKRLDAGE 
Sbjct: 2   AITLPAGMKITGEILPAYEDILTPAALALVDKLHRAFEPRRQELLAARVERTKRLDAGEL 61

Query: 70  PDFLAETKSVRDGDWTIAPLPQDLQCRRVEITGPVERKMIINALNSGADSYMTDFEDSNA 129
           PDFL +TKSVR+GDW +AP+P  L CRRVEITGPVE KM+INA NSGADSYMTDFEDSN 
Sbjct: 62  PDFLPQTKSVREGDWKVAPVPPALHCRRVEITGPVEAKMVINAFNSGADSYMTDFEDSNT 121

Query: 130 PSWDNQITGHINLKDAVRRTISLEQNGKSYTLNDKVATLIVRPRGWHLDEKHVKVDGKRV 189
           P+W NQ+ G +NLK AVRRT++L+ NGK Y LN K+ATL VRPRGWHLDEKHV +DG+RV
Sbjct: 122 PNWHNQLQGQVNLKAAVRRTLTLDSNGKHYKLNGKIATLQVRPRGWHLDEKHVTIDGQRV 181

Query: 190 SGGIFDFALFMVHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEAVGVPRGTIR 249
           SGGIFDFALF+ HNAKE +ARG+GP+FYLPKMESHLEARLWND+FV AQ  +G+P+GT++
Sbjct: 182 SGGIFDFALFLFHNAKEQIARGAGPFFYLPKMESHLEARLWNDVFVMAQNEIGLPQGTVK 241

Query: 250 ATVLIETIVAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKADRDFCLADRSQITMT 309
           ATVLIETI+AAFEM+EILYELREHS+GLNAGRWDYIFS IKKFK D++FCLADR+++TMT
Sbjct: 242 ATVLIETILAAFEMEEILYELREHSAGLNAGRWDYIFSCIKKFKVDKNFCLADRAKVTMT 301

Query: 310 SPFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMSGVRSDKARDAGDGYDG 369
           +PFMR+YALLLLKTCH+R APAIGGMSALIPIKNDP  N  AM G+ +DK RDA DGYDG
Sbjct: 302 APFMRSYALLLLKTCHKRGAPAIGGMSALIPIKNDPEKNAIAMQGIINDKKRDATDGYDG 361

Query: 370 GWVAHPGLVPIAMEEFVKVLGDKPNQIGKQRDDVLVTATDLTDFRPEAPITEGGLRNNIN 429
           GWVAHPGLV  AM+EFV VLGDKPNQ  KQRDDV V A DL DF+PE PITE GLR NIN
Sbjct: 362 GWVAHPGLVEPAMKEFVAVLGDKPNQFDKQRDDVNVAAKDLLDFQPETPITEAGLRMNIN 421

Query: 430 VGIHYLGAWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRKVTAELVREL 489
           VGIHYLG+WLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRKVTAE+VR L
Sbjct: 422 VGIHYLGSWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRKVTAEMVRAL 481

Query: 490 SAQELEKVKQAVGGDTKPYERAAQIFEEMSTSEQFTDFLTLPLYEEI 536
             +EL KVK  VGGDT  Y+RA +IFE+MSTSE F +FLTLPLYEEI
Sbjct: 482 IPEELAKVKAFVGGDTTTYDRAGEIFEQMSTSEDFAEFLTLPLYEEI 528


Lambda     K      H
   0.318    0.134    0.397 

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: 821
Number of extensions: 24
Number of successful extensions: 2
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: 536
Length of database: 528
Length adjustment: 35
Effective length of query: 501
Effective length of database: 493
Effective search space:   246993
Effective search space used:   246993
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate RR42_RS12175 RR42_RS12175 (malate synthase)
to HMM TIGR01344 (aceB: malate synthase A (EC 2.3.3.9))

# 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.carbon/TIGR01344.hmm
# target sequence database:        /tmp/gapView.9386.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01344  [M=511]
Accession:   TIGR01344
Description: malate_syn_A: malate synthase A
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.9e-226  736.3   0.0   7.8e-226  736.1   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS12175  RR42_RS12175 malate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS12175  RR42_RS12175 malate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  736.1   0.0  7.8e-226  7.8e-226       1     510 [.      22     528 .]      22     528 .] 0.99

  Alignments for each domain:
  == domain 1  score: 736.1 bits;  conditional E-value: 7.8e-226
                                 TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrv 69 
                                               +lt++al+++ +lhr f++rr+ella+r ++  +ld+gel+dflp+tk++re+dwkva++p++l  rrv
  lcl|FitnessBrowser__Cup4G11:RR42_RS12175  22 ILTPAALALVDKLHRAFEPRRQELLAARVERTKRLDAGELPDFLPQTKSVREGDWKVAPVPPALHCRRV 90 
                                               79******************************************************************* PP

                                 TIGR01344  70 eitGPvdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkakl 138
                                               eitGPv+ kmvina+n++a  +++dfeds++P w+n ++Gq+nlk a+r++++    ++gk+y+l+ k 
  lcl|FitnessBrowser__Cup4G11:RR42_RS12175  91 EITGPVEAKMVINAFNSGADSYMTDFEDSNTPNWHNQLQGQVNLKAAVRRTLTLD--SNGKHYKLNGKI 157
                                               ****************************************************998..7*********** PP

                                 TIGR01344 139 avlivrprGwhlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvf 207
                                               a+l vrprGwhl e+h++idg+ +sg ++df+l++fhna+e++++G GP+fylPk+eshlearlwndvf
  lcl|FitnessBrowser__Cup4G11:RR42_RS12175 158 ATLQVRPRGWHLDEKHVTIDGQRVSGGIFDFALFLFHNAKEQIARGAGPFFYLPKMESHLEARLWNDVF 226
                                               ********************************************************************* PP

                                 TIGR01344 208 llaqevlglprGtikatvlietlpaafemdeilyelrehssGlncGrwdyifslikklkkaeevvlPdr 276
                                               ++aq+++glp+Gt+katvliet+ aafem+eilyelrehs+Gln+Grwdyifs+ikk+k ++++ l dr
  lcl|FitnessBrowser__Cup4G11:RR42_RS12175 227 VMAQNEIGLPQGTVKATVLIETILAAFEMEEILYELREHSAGLNAGRWDYIFSCIKKFKVDKNFCLADR 295
                                               ********************************************************************* PP

                                 TIGR01344 277 davtmdkaflnaysklliqtchrrgafalGGmaafiPikddpaaneaalekvradkereaknGhdGtwv 345
                                                +vtm+++f+++y+ ll++tch+rga a+GGm+a iPik+dp+ n  a++ + +dk+r+a++G+dG wv
  lcl|FitnessBrowser__Cup4G11:RR42_RS12175 296 AKVTMTAPFMRSYALLLLKTCHKRGAPAIGGMSALIPIKNDPEKNAIAMQGIINDKKRDATDGYDGGWV 364
                                               ********************************************************************* PP

                                 TIGR01344 346 ahPdlvevalevfdevlge.pnqldrvrledvsitaaellev.kdasrteeGlrenirvglryieawlr 412
                                               ahP+lve a++ f +vlg+ pnq d++r +dv+++a +ll+  +++  te+Glr ni+vg++y+ +wl 
  lcl|FitnessBrowser__Cup4G11:RR42_RS12175 365 AHPGLVEPAMKEFVAVLGDkPNQFDKQR-DDVNVAAKDLLDFqPETPITEAGLRMNINVGIHYLGSWLA 432
                                               ******************999*****88.************9789999********************* PP

                                 TIGR01344 413 GsGavpiynlmedaataeisraqlwqwikhGv.vledGekvtselvrdllkeeleklkkesgkeeyaka 480
                                               G+G+vpi+nlmedaataeisr+q+wqwi+  +  ledG+kvt+e+vr l+ eel+k+k  +g +    +
  lcl|FitnessBrowser__Cup4G11:RR42_RS12175 433 GNGCVPIHNLMEDAATAEISRSQVWQWIRSPKgKLEDGRKVTAEMVRALIPEELAKVKAFVGGDT---T 498
                                               *****************************97636**************************99988...8 PP

                                 TIGR01344 481 rleeaaellerlvlseeledfltlpaydel 510
                                                +++a e++e++++se++++fltlp+y+e+
  lcl|FitnessBrowser__Cup4G11:RR42_RS12175 499 TYDRAGEIFEQMSTSEDFAEFLTLPLYEEI 528
                                               9**************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (528 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.48
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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