Alignments for a candidate for glcB in Cupriavidus basilensis 4G11

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.13166.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.11
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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

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 catabolism of small carbon sources