Alignments for a candidate for aceA in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Sinorhizobium meliloti 1021

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate SMc00768 SMc00768 isocitrate lyase

Query= BRENDA::Q8RPZ0
         (436 letters)



>FitnessBrowser__Smeli:SMc00768
          Length = 429

 Score =  556 bits (1434), Expect = e-163
 Identities = 278/414 (67%), Positives = 329/414 (79%), Gaps = 4/414 (0%)

Query: 26  ATEPRWRDIERTYGAEEVIRLSGSVREEHTLARRGADRLWRQLHELDYVHALGALTGGQA 85
           A E R+  IER Y AE+V RL GSV   ++LA  GA+RLW+ +HE D+V+ALGAL+G QA
Sbjct: 11  APEGRFDGIERPYSAEDVKRLRGSVEIRYSLAEMGANRLWKLIHEEDFVNALGALSGNQA 70

Query: 86  VQQVRAGLQAIYLFGWQVAADANQAGHTYPDQSLYPANSVPQVVRRINNALLRADQIATA 145
           +Q VRAGL+AIYL GWQVAADAN A   YPDQSLYPAN+ P++ +RIN  L RADQI TA
Sbjct: 71  MQMVRAGLKAIYLSGWQVAADANTASAMYPDQSLYPANAAPELAKRINRTLQRADQIETA 130

Query: 146 ENAGDGTD-WLAPIVADAEAGFGGPLNAFELTKAMIEAGAAGIHYEDQLASEKKCGHLGG 204
           E  G   + W APIVADAEAGFGGPLNAFE+ KA IEAGAAG+HYEDQLASEKKCGHLGG
Sbjct: 131 EGKGLSVETWFAPIVADAEAGFGGPLNAFEIMKAFIEAGAAGVHYEDQLASEKKCGHLGG 190

Query: 205 KVLVPTAQHIRTLNAARLAADIADVPTVIIARTDALAASLITSDVDERDAEFLTGE--RT 262
           KVL+PTA HIR LNAARLAAD+   PT++IARTDA AA L+TSD+DERD  F+  +  RT
Sbjct: 191 KVLIPTAAHIRNLNAARLAADVMGTPTLVIARTDAEAAKLLTSDIDERDRPFVDYDAGRT 250

Query: 263 AEGFHRVRNGMAPVIARGLAYAPYADLLWMETGTPDLAQAREFAEAIHAQYPEQLLAYNC 322
            EGF++V+NG+ P IAR +AYAP+ DL+W ET  PDL QAR+FAE +H  +P +LLAYNC
Sbjct: 251 VEGFYQVKNGIEPCIARAIAYAPHCDLIWCETSKPDLEQARKFAEGVHKAHPGKLLAYNC 310

Query: 323 SPSFNWRAALDDDRIAKFQRELGAMGYRFQFITLAGFHSLNHAMFDLARGYAEHGMTAYV 382
           SPSFNW+  LDD  IAKFQRELGAMGY+FQFITLAGFH LN+ MF+LARGY +  M AY 
Sbjct: 311 SPSFNWKKNLDDATIAKFQRELGAMGYKFQFITLAGFHQLNYGMFELARGYRDRQMAAYS 370

Query: 383 DLQEREFAAQADGFTAVRHQREVGTGYFDLVSTAVNPA-SSTTALSGSTEEEQF 435
           +LQE EFAA+A+G+TA +HQREVGTGYFD VS A+    SSTTA+  STE +QF
Sbjct: 371 ELQEAEFAAEANGYTATKHQREVGTGYFDAVSVAITGGQSSTTAMKESTEHDQF 424


Lambda     K      H
   0.318    0.131    0.388 

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: 561
Number of extensions: 25
Number of successful extensions: 4
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: 436
Length of database: 429
Length adjustment: 32
Effective length of query: 404
Effective length of database: 397
Effective search space:   160388
Effective search space used:   160388
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: 51 (24.3 bits)

Align candidate SMc00768 SMc00768 (isocitrate lyase)
to HMM TIGR01346 (aceA: isocitrate lyase (EC 4.1.3.1))

# 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.aa/TIGR01346.hmm
# target sequence database:        /tmp/gapView.26262.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01346  [M=527]
Accession:   TIGR01346
Description: isocit_lyase: isocitrate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     3e-179  582.7   1.5    9.3e-98  313.8   0.0    2.0  2  lcl|FitnessBrowser__Smeli:SMc00768  SMc00768 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00768  SMc00768 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.8   0.0   9.3e-98   9.3e-98      12     252 ..      14     243 ..      10     244 .. 0.97
   2 !  270.7   0.4   1.1e-84   1.1e-84     347     527 .]     242     424 ..     241     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 313.8 bits;  conditional E-value: 9.3e-98
                           TIGR01346  12 drwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvqvsqqaka.ldavyls 85 
                                          r+++i+r+ysa+dv +lrGsv+ +  l++++a++lw+++++e+     +++lGal ++q++q+++a l+a+yls
  lcl|FitnessBrowser__Smeli:SMc00768  14 GRFDGIERPYSAEDVKRLRGSVEIRYSLAEMGANRLWKLIHEED----FVNALGALSGNQAMQMVRAgLKAIYLS 84 
                                         69*********************9999*************9775....59************************* PP

                           TIGR01346  86 GWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkelyidylvPivadadaG 160
                                         GWqv++dan+++ ++Pd+++yPa++ P+  +r++++l+++d++++ +++  + e         ++ Pivada+aG
  lcl|FitnessBrowser__Smeli:SMc00768  85 GWQVAADANTASAMYPDQSLYPANAAPELAKRINRTLQRADQIETAEGKGLSVE--------TWFAPIVADAEAG 151
                                         *********************************************999988887........6************ PP

                           TIGR01346 161 fGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllvartdae 235
                                         fGG l++f+++k++ie+Gaagvh+edql+sekkCGhl+Gkvl+p+  h+++l+aarlaadvmg++tl++artdae
  lcl|FitnessBrowser__Smeli:SMc00768 152 FGGPLNAFEIMKAFIEAGAAGVHYEDQLASEKKCGHLGGKVLIPTAAHIRNLNAARLAADVMGTPTLVIARTDAE 226
                                         *************************************************************************** PP

                           TIGR01346 236 aatlitsdvdardhefi 252
                                         aa+l+tsd+d+rd++f+
  lcl|FitnessBrowser__Smeli:SMc00768 227 AAKLLTSDIDERDRPFV 243
                                         ***************97 PP

  == domain 2  score: 270.7 bits;  conditional E-value: 1.1e-84
                           TIGR01346 347 ffdwelertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnW 421
                                         f d++  rt eGfy+vk+g+e++i+ra a+aP+ dl+W+ets+Pdle+a++faegv++ +P+kllayn+sPsfnW
  lcl|FitnessBrowser__Smeli:SMc00768 242 FVDYDAGRTVEGFYQVKNGIEPCIARAIAYAPHCDLIWCETSKPDLEQARKFAEGVHKAHPGKLLAYNCSPSFNW 316
                                         89************************************************************************* PP

                           TIGR01346 422 dkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel...edGvdvlkhq 493
                                         +k+l+d +i+kf++elg++GykfqfitlaG+h  ++++f+la+++  + m ay e +q+ e+    +G+++ khq
  lcl|FitnessBrowser__Smeli:SMc00768 317 KKNLDDATIAKFQRELGAMGYKFQFITLAGFHQLNYGMFELARGYRDRQMAAYSE-LQEAEFaaeANGYTATKHQ 390
                                         ******************************************************9.******9999********* PP

                           TIGR01346 494 kesGaeyfdqllklvqgGvsataalaksveedqf 527
                                         +e+G++yfd +   + gG s+t+a+++s+e dqf
  lcl|FitnessBrowser__Smeli:SMc00768 391 REVGTGYFDAVSVAITGGQSSTTAMKESTEHDQF 424
                                         *********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (429 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: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 3.82
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis