Alignments for a candidate for glcB in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Caulobacter crescentus NA1000

Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate CCNA_01843 CCNA_01843 malate synthase

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



>FitnessBrowser__Caulo:CCNA_01843
          Length = 525

 Score =  553 bits (1424), Expect = e-162
 Identities = 279/526 (53%), Positives = 368/526 (69%), Gaps = 7/526 (1%)

Query: 11  LQLPQGMEITAEIKPGYDAILSREALELVAALHRTFEPRRQQLLQARAERTKRLDAGERP 70
           L +   +++TA ++     +L+ EAL  VA LHR F+ RR+QLL+AR  R  R DAGE P
Sbjct: 3   LDIAANIQVTAPVEGRAAEVLTPEALAFVADLHRRFDARRRQLLEARQARQARFDAGELP 62

Query: 71  DFLAETKSVRDGDWTIAPLPQDLQCRRVEITGPVERKMIINALNSGADSYMTDFEDSNAP 130
           DFL ET S+R  DWTIA +P DL  RRVEITGPV RKMIINALN GA  +M DFED+ AP
Sbjct: 63  DFLDETASIRSADWTIAAIPSDLLDRRVEITGPVNRKMIINALNCGAKVFMADFEDATAP 122

Query: 131 SWDNQITGHINLKDAVRRTISL--EQNGKSYTLNDKVATLIVRPRGWHLDEKHVKVDGKR 188
           +W N + G INLKD  +  ++    ++GK+Y +    A L +RPRGWHL E+H++VDG+ 
Sbjct: 123 TWANVVEGQINLKDRWQGELTHVDAKSGKAYAMGPTSAVLKIRPRGWHLMERHLEVDGQA 182

Query: 189 VSGGIFDFALFMVHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEAVGVPRGTI 248
           V+G +FDF L+  HNAK  +A+GSGPYFYLPK+ESHLEARLWND+F+ AQE + +P GTI
Sbjct: 183 VAGALFDFGLYAFHNAKAAIAKGSGPYFYLPKLESHLEARLWNDVFIRAQEVLDLPVGTI 242

Query: 249 RATVLIETIVAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKADRDFCLADRSQITM 308
           +ATVLIETI AAFEMDEIL+EL++H  GLN GRWDYIFS IK+      F   DRS + M
Sbjct: 243 KATVLIETIPAAFEMDEILFELKDHIVGLNCGRWDYIFSFIKRLGRREAFLTPDRSAMVM 302

Query: 309 TSPFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMSGVRSDKARDAGDGYD 368
              F+ AY+L L++TCHRR A A+GGM+A IP+K D AAN+ A + VR+DK R+AG G+D
Sbjct: 303 GKAFLGAYSLKLIQTCHRRGAFAMGGMAAQIPVKGDEAANNAAFAKVRADKEREAGAGHD 362

Query: 369 GGWVAHPGLVPIAMEEFVKVLGDKPNQIGKQRDDVLVTATDLTDFRPEAPITEGGLRNNI 428
           G WVAHP LVP+AME F +++   PNQ+ ++ DD+ +T   + +   E   TE G+R NI
Sbjct: 363 GTWVAHPDLVPVAMEVFNRLM-PTPNQLDRKLDDLSITQAQMLELH-EGSRTEAGVRENI 420

Query: 429 NVGIHYLGAWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRKVTAELVRE 488
            VG+ Y  AW+ G G VP++NLMEDAATAEI R+Q+WQW+R     L+DGR +++EL   
Sbjct: 421 RVGVRYTQAWIEGRGAVPLYNLMEDAATAEICRTQLWQWVRL-GAALDDGRVLSSELFVS 479

Query: 489 LSAQELEKVKQAVGGDTKPYERAAQIFEEMSTSEQFTDFLTLPLYE 534
           L +QE+  +++     +   E AA IF  M  S+   +FLT+P YE
Sbjct: 480 LFSQEMSDLRREFA--SPRLEEAAHIFTRMVLSDDLEEFLTIPAYE 523


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: 696
Number of extensions: 23
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: 536
Length of database: 525
Length adjustment: 35
Effective length of query: 501
Effective length of database: 490
Effective search space:   245490
Effective search space used:   245490
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 CCNA_01843 CCNA_01843 (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.17071.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-277  905.8   0.1   3.3e-277  905.6   0.1    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01843  CCNA_01843 malate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01843  CCNA_01843 malate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  905.6   0.1  3.3e-277  3.3e-277       1     510 [.      22     525 .]      22     525 .] 1.00

  Alignments for each domain:
  == domain 1  score: 905.6 bits;  conditional E-value: 3.3e-277
                             TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrveitG 73 
                                           vlt+eal+f+a+lhrrf++rr++ll++r+++qa++d+gel+dfl+et++ir++dw++aaip+dlldrrveitG
  lcl|FitnessBrowser__Caulo:CCNA_01843  22 VLTPEALAFVADLHRRFDARRRQLLEARQARQARFDAGELPDFLDETASIRSADWTIAAIPSDLLDRRVEITG 94 
                                           89*********************************************************************** PP

                             TIGR01344  74 PvdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkaklavlivrpr 146
                                           Pv+rkm+inaln++akvf+adfed+++Ptw+nvveGqinlkd+++ge++++d++sgk+ya+ +++avl++rpr
  lcl|FitnessBrowser__Caulo:CCNA_01843  95 PVNRKMIINALNCGAKVFMADFEDATAPTWANVVEGQINLKDRWQGELTHVDAKSGKAYAMGPTSAVLKIRPR 167
                                           ************************************************************************* PP

                             TIGR01344 147 GwhlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvfllaqevlglprG 219
                                           Gwhl+erhle+dg+a++g+l+dfgly+fhna+++++kG+GPyfylPkleshlearlwndvf++aqevl+lp+G
  lcl|FitnessBrowser__Caulo:CCNA_01843 168 GWHLMERHLEVDGQAVAGALFDFGLYAFHNAKAAIAKGSGPYFYLPKLESHLEARLWNDVFIRAQEVLDLPVG 240
                                           ************************************************************************* PP

                             TIGR01344 220 tikatvlietlpaafemdeilyelrehssGlncGrwdyifslikklkkaeevvlPdrdavtmdkaflnayskl 292
                                           tikatvliet+paafemdeil+el++h++GlncGrwdyifs+ik+l ++e++++Pdr+a++m+kafl ays +
  lcl|FitnessBrowser__Caulo:CCNA_01843 241 TIKATVLIETIPAAFEMDEILFELKDHIVGLNCGRWDYIFSFIKRLGRREAFLTPDRSAMVMGKAFLGAYSLK 313
                                           ************************************************************************* PP

                             TIGR01344 293 liqtchrrgafalGGmaafiPikddpaaneaalekvradkereaknGhdGtwvahPdlvevalevfdevlgep 365
                                           liqtchrrgafa+GGmaa+iP+k+d+aan+aa++kvradkerea +GhdGtwvahPdlv+va+evf++++++p
  lcl|FitnessBrowser__Caulo:CCNA_01843 314 LIQTCHRRGAFAMGGMAAQIPVKGDEAANNAAFAKVRADKEREAGAGHDGTWVAHPDLVPVAMEVFNRLMPTP 386
                                           ************************************************************************* PP

                             TIGR01344 366 nqldrvrledvsitaaellevkdasrteeGlrenirvglryieawlrGsGavpiynlmedaataeisraqlwq 438
                                           nqldr +l+d+sit+a++le++++srte+G+renirvg+ry++aw++G+Gavp+ynlmedaataei+r+qlwq
  lcl|FitnessBrowser__Caulo:CCNA_01843 387 NQLDR-KLDDLSITQAQMLELHEGSRTEAGVRENIRVGVRYTQAWIEGRGAVPLYNLMEDAATAEICRTQLWQ 458
                                           ****9.77***************************************************************** PP

                             TIGR01344 439 wikhGvvledGekvtselvrdllkeeleklkkesgkeeyakarleeaaellerlvlseeledfltlpaydel 510
                                           w++ G++l+dG++++sel+++l+++e+++l++e     +a++rleeaa++++r+vls++le+flt+pay+ l
  lcl|FitnessBrowser__Caulo:CCNA_01843 459 WVRLGAALDDGRVLSSELFVSLFSQEMSDLRRE-----FASPRLEEAAHIFTRMVLSDDLEEFLTIPAYELL 525
                                           *******************************99.....*******************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (525 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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Protein sequences (fasta format)
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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