GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcB in Azospirillum brasilense Sp245

Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate AZOBR_RS03245 AZOBR_RS03245 malate synthase

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



>FitnessBrowser__azobra:AZOBR_RS03245
          Length = 534

 Score =  623 bits (1607), Expect = 0.0
 Identities = 315/526 (59%), Positives = 388/526 (73%), Gaps = 8/526 (1%)

Query: 16  GMEITAEIKPGYDAILSREALELVAALHRTFEPRRQQLLQARAERTKRLDAGERPDFLAE 75
           G+EI   I PG + IL+ EAL  +A L   F   R +LL  R +R   +D G RPDFL E
Sbjct: 7   GLEILGPITPGVETILTPEALAFLAELEGRFGSERLRLLDVRTKRRALIDQGHRPDFLPE 66

Query: 76  TKSVRDGDWTIAPLPQDLQCRRVEITGPVERKMIINALNSGADSYMTDFEDSNAPSWDNQ 135
           T+++R+ DWTIAPLP DL  RRVEITGPV+RKM+INALNSGA  +M DFEDS+ PSW N 
Sbjct: 67  TRAIREADWTIAPLPHDLLDRRVEITGPVDRKMVINALNSGAKVFMADFEDSSCPSWANL 126

Query: 136 ITGHINLKDAVRRTISLEQ--NGKSYTLNDKVATLIVRPRGWHLDEKHVKVDGKRVSGGI 193
           I G  NL+DAVRRTI+ +   +GK Y LNDK A L VRPRGWHL EKHV+ DG+ VSG +
Sbjct: 127 IEGQANLRDAVRRTIAFDDPVSGKKYRLNDKTAVLKVRPRGWHLAEKHVRFDGEPVSGAL 186

Query: 194 FDFALFMVHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEAVGVPRGTIRATVL 253
           FDFAL+  HNA+EL+ARGSGPYFYLPK+ESH EARLWN++F  A++ + +P G+I+ATVL
Sbjct: 187 FDFALYAFHNAQELLARGSGPYFYLPKLESHFEARLWNEVFSVAEDYLKIPHGSIKATVL 246

Query: 254 IETIVAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKADRDFCLADRSQITMTSPFM 313
           +ETI+AAFEMDEILYELR+HS+GLN GRWDYIFS IK F+ D    L DR+++TM +PF+
Sbjct: 247 VETILAAFEMDEILYELRDHSAGLNCGRWDYIFSFIKTFRNDPAAVLPDRAEVTMATPFL 306

Query: 314 RAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMSGVRSDKARDAGDGYDGGWVA 373
           ++Y+LL +KTCHRR APAIGGM+A IP+K+DPAAN+ A S VR+DK R+  +G+DG WVA
Sbjct: 307 QSYSLLAVKTCHRRGAPAIGGMAAYIPVKDDPAANETAFSKVRADKEREVSNGHDGTWVA 366

Query: 374 HPGLVPIAMEEFVKVLGDKPNQIGKQRDDVLVTATDLTDFRPEAPITEGGLRNNINVGIH 433
           HPGLVP+A E F   +  KPNQI ++R DV VTA DL    PE P TE GLRNN+ V I 
Sbjct: 367 HPGLVPVAREVFDAYM-RKPNQIDRKRADVSVTAADLLAV-PEGPKTERGLRNNVAVAIG 424

Query: 434 YLGAWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRKVTAELVRELSAQE 493
           YL AWL G GCVP+ NLMEDAATAEISR+Q+WQW+   +  L+DGR VT ELV E  A+E
Sbjct: 425 YLEAWLRGIGCVPLFNLMEDAATAEISRTQLWQWVHH-RATLDDGRPVTMELVDETIAEE 483

Query: 494 LEKVKQAVGG---DTKPYERAAQIFEEMSTSEQFTDFLTLPLYEEI 536
           L   K  VG    D   YE AA +  ++   + F DFLTLP Y+ I
Sbjct: 484 LAAWKARVGDRAFDHGLYEEAAVMLRDLVERDDFVDFLTLPAYDRI 529


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: 735
Number of extensions: 29
Number of successful extensions: 5
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: 534
Length adjustment: 35
Effective length of query: 501
Effective length of database: 499
Effective search space:   249999
Effective search space used:   249999
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 AZOBR_RS03245 AZOBR_RS03245 (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.3498.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-253  827.2   0.0   2.2e-253  827.0   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS03245  AZOBR_RS03245 malate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS03245  AZOBR_RS03245 malate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  827.0   0.0  2.2e-253  2.2e-253       1     510 [.      21     529 ..      21     530 .. 1.00

  Alignments for each domain:
  == domain 1  score: 827.0 bits;  conditional E-value: 2.2e-253
                                 TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrv 69 
                                               +lt+eal+flael  rf + r +ll+ r+k++a +d+g+++dflpet++ire+dw++a++p+dlldrrv
  lcl|FitnessBrowser__azobra:AZOBR_RS03245  21 ILTPEALAFLAELEGRFGSERLRLLDVRTKRRALIDQGHRPDFLPETRAIREADWTIAPLPHDLLDRRV 89 
                                               89******************************************************************* PP

                                 TIGR01344  70 eitGPvdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkakl 138
                                               eitGPvdrkmvinaln++akvf+adfedss+P+w+n++eGq nl+da+r++i f d+ sgk+y+l+ k+
  lcl|FitnessBrowser__azobra:AZOBR_RS03245  90 EITGPVDRKMVINALNSGAKVFMADFEDSSCPSWANLIEGQANLRDAVRRTIAFDDPVSGKKYRLNDKT 158
                                               ********************************************************************* PP

                                 TIGR01344 139 avlivrprGwhlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvf 207
                                               avl+vrprGwhl e+h+  dg+++sg+l+df+ly+fhna+ell++G+GPyfylPklesh earlwn+vf
  lcl|FitnessBrowser__azobra:AZOBR_RS03245 159 AVLKVRPRGWHLAEKHVRFDGEPVSGALFDFALYAFHNAQELLARGSGPYFYLPKLESHFEARLWNEVF 227
                                               ********************************************************************* PP

                                 TIGR01344 208 llaqevlglprGtikatvlietlpaafemdeilyelrehssGlncGrwdyifslikklkkaeevvlPdr 276
                                                +a+++l +p+G+ikatvl+et+ aafemdeilyelr+hs+GlncGrwdyifs+ik+++++++ vlPdr
  lcl|FitnessBrowser__azobra:AZOBR_RS03245 228 SVAEDYLKIPHGSIKATVLVETILAAFEMDEILYELRDHSAGLNCGRWDYIFSFIKTFRNDPAAVLPDR 296
                                               ********************************************************************* PP

                                 TIGR01344 277 davtmdkaflnaysklliqtchrrgafalGGmaafiPikddpaaneaalekvradkereaknGhdGtwv 345
                                                 vtm ++fl++ys l ++tchrrga a+GGmaa+iP+kddpaane+a++kvradkere++nGhdGtwv
  lcl|FitnessBrowser__azobra:AZOBR_RS03245 297 AEVTMATPFLQSYSLLAVKTCHRRGAPAIGGMAAYIPVKDDPAANETAFSKVRADKEREVSNGHDGTWV 365
                                               ********************************************************************* PP

                                 TIGR01344 346 ahPdlvevalevfdevlgepnqldrvrledvsitaaellevkdasrteeGlrenirvglryieawlrGs 414
                                               ahP+lv+va+evfd+++ +pnq+dr+r +dvs+taa+ll+v+++ +te+Glr+n+ v++ y+eawlrG 
  lcl|FitnessBrowser__azobra:AZOBR_RS03245 366 AHPGLVPVAREVFDAYMRKPNQIDRKR-ADVSVTAADLLAVPEGPKTERGLRNNVAVAIGYLEAWLRGI 433
                                               *************************88.***************************************** PP

                                 TIGR01344 415 GavpiynlmedaataeisraqlwqwikhGvvledGekvtselvrdllkeeleklkkesgkeeyakarle 483
                                               G+vp++nlmedaataeisr+qlwqw++h ++l+dG+ vt elv + ++eel++ k  +g+  + ++ +e
  lcl|FitnessBrowser__azobra:AZOBR_RS03245 434 GCVPLFNLMEDAATAEISRTQLWQWVHHRATLDDGRPVTMELVDETIAEELAAWKARVGDRAFDHGLYE 502
                                               ********************************************************************* PP

                                 TIGR01344 484 eaaellerlvlseeledfltlpaydel 510
                                               eaa +l  lv  +++ dfltlpayd++
  lcl|FitnessBrowser__azobra:AZOBR_RS03245 503 EAAVMLRDLVERDDFVDFLTLPAYDRI 529
                                               *************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 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: 7.43
//
[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