Alignments for a candidate for glcB in Azospirillum brasilense Sp245

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.1046.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: 0.02u 0.02s 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:

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