GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Caulobacter crescentus NA1000

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate CCNA_03206 CCNA_03206 L-serine dehydratase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4954
         (458 letters)



>FitnessBrowser__Caulo:CCNA_03206
          Length = 462

 Score =  488 bits (1256), Expect = e-142
 Identities = 257/464 (55%), Positives = 335/464 (72%), Gaps = 8/464 (1%)

Query: 1   MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALVDHGFLADVRRVEIRLYGSLSATGVG 60
           M  SVFDLFK+G+GPSSSHT+GPM AA  F   L D G LA V RVE RLY SL+ TG G
Sbjct: 1   MTASVFDLFKLGVGPSSSHTMGPMTAAVLFIGRLRDAGKLAAVARVETRLYASLALTGRG 60

Query: 61  HATDRACVMGLMGEWPDRIDPTTIDSRIHTLRETGKLCLAGVAQIAFDWQRDLLLLD-ES 119
           HATDRA ++GLMG  P  +DP   ++ +   + +  L L G   IAFD  RD++ L  E 
Sbjct: 61  HATDRAVILGLMGFVPADLDPDAGEAALLDCQASQSLKLGGEVDIAFDEARDIVWLGHER 120

Query: 120 LPYHPNAMSLTAFGETGE-LFEQTYYSVGGGFIIEAAEAESGIAPAGDVVLPYDFSSAAE 178
           LP HPNA++  A+ + G+ L E+TY+S+GGGF+ + AE      P     +P+ F SAA+
Sbjct: 121 LPQHPNALTFAAYDKAGQVLAERTYFSIGGGFVRDEAEMGRNAPPDEGPAIPFPFESAAD 180

Query: 179 LLKLCNEHGLRVGELMMANERAWRSDAEIRQGLLHIWSVMRECVEQGLRHEGILPGGLSV 238
           LL+   + GL + E+M ANERA  S  E+  GL  I+  M  C+++G+R EG+LPGGL+V
Sbjct: 181 LLERAEQAGLSIAEVMAANERARMSQGEMDAGLDRIFGAMEACIDRGMRQEGVLPGGLTV 240

Query: 239 PRRAAKLHRSLQEIGKPNVITSTLSAMEWVNLYALAVNEENAAGGRMVTAPTNGAAGIIP 298
            RRA ++H+++Q       ++  L+AM++VNL+A+AVNEENAAGGR+VTAPTNGAAG+IP
Sbjct: 241 KRRARQIHQTIQG-RMERQMSDPLAAMDFVNLWAMAVNEENAAGGRVVTAPTNGAAGLIP 299

Query: 299 AVLHYYMKFNADASDDDVVAFFLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGL 358
           AVL ++++F    + + +  F L AAA+G L K+NASISGAEVGCQGEVG AC+MAAAGL
Sbjct: 300 AVLRFFVRFYK-GTPEQIRTFLLTAAAIGALYKRNASISGAEVGCQGEVGVACSMAAAGL 358

Query: 359 AEVLGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGD 418
           A  LG T  Q+ENAAEIG+EHNLGLTCDP+GGLVQ+PCIERNA+ A+KAI+A ++AL GD
Sbjct: 359 AAALGGTNAQIENAAEIGMEHNLGLTCDPIGGLVQIPCIERNAMGAIKAIDAARLALLGD 418

Query: 419 GKHFISLDRVIRTMRDTGADMHDKYKETSRGGLA----VNWVEC 458
           G+H +SLD+VI TM+ TG DM++ YKETS GGLA    VN VEC
Sbjct: 419 GQHSVSLDKVIATMKRTGEDMNEIYKETSMGGLAVGLSVNRVEC 462


Lambda     K      H
   0.320    0.135    0.404 

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: 539
Number of extensions: 19
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: 458
Length of database: 462
Length adjustment: 33
Effective length of query: 425
Effective length of database: 429
Effective search space:   182325
Effective search space used:   182325
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate CCNA_03206 CCNA_03206 (L-serine dehydratase)
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

# 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/TIGR00720.hmm
# target sequence database:        /tmp/gapView.27988.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00720  [M=450]
Accession:   TIGR00720
Description: sda_mono: L-serine ammonia-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-202  658.6   0.2     3e-202  658.4   0.2    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03206  CCNA_03206 L-serine dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03206  CCNA_03206 L-serine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  658.4   0.2    3e-202    3e-202       2     448 ..       4     453 ..       3     455 .. 0.98

  Alignments for each domain:
  == domain 1  score: 658.4 bits;  conditional E-value: 3e-202
                             TIGR00720   2 svfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelp 74 
                                           svfdlfk+G+GPsssht+GPm aa  f+ +l+++gkl++v+rv+  ly slaltG+Gh+td+av+lGl+G+ p
  lcl|FitnessBrowser__Caulo:CCNA_03206   4 SVFDLFKLGVGPSSSHTMGPMTAAVLFIGRLRDAGKLAAVARVETRLYASLALTGRGHATDRAVILGLMGFVP 76 
                                           9************************************************************************ PP

                             TIGR00720  75 eevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevlkektyysvG 146
                                            ++d +  e+ l +++++++lkl+++ +i fd+++d++   +e lp+h+n+l++ ayd++g+vl+e+ty+s+G
  lcl|FitnessBrowser__Caulo:CCNA_03206  77 ADLDPDAGEAALLDCQASQSLKLGGEVDIAFDEARDIVWLgHERLPQHPNALTFAAYDKAGQVLAERTYFSIG 149
                                           *************************************9988******************************** PP

                             TIGR00720 147 GGfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmee 217
                                           GGf+ de+e+++++  +e   +p+pf+saa+lle  ++ glsi+ev+ +ne a  s+ e++a l +i+ +me+
  lcl|FitnessBrowser__Caulo:CCNA_03206 150 GGFVRDEAEMGRNAPPDEgpAIPFPFESAADLLERAEQAGLSIAEVMAANERARMSQGEMDAGLDRIFGAMEA 222
                                           **************9998899**************************************************** PP

                             TIGR00720 218 cierglkaegvlpGglkvkrraaslkrklkakeets.kdplavldwvnlyalavneenaaGgrvvtaPtnGaa 289
                                           ci+rg+++egvlpGgl vkrra ++++ ++ + e + +dpla++d+vnl+a+avneenaaGgrvvtaPtnGaa
  lcl|FitnessBrowser__Caulo:CCNA_03206 223 CIDRGMRQEGVLPGGLTVKRRARQIHQTIQGRMERQmSDPLAAMDFVNLWAMAVNEENAAGGRVVTAPTNGAA 295
                                           ******************************99888779*********************************** PP

                             TIGR00720 290 giiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpe 362
                                           g+iPavl+++ +f +  + e++  fllta+aiG+lyk+nasisgaevGCqgevGvacsmaaagla++lggt  
  lcl|FitnessBrowser__Caulo:CCNA_03206 296 GLIPAVLRFFVRFYKG-TPEQIRTFLLTAAAIGALYKRNASISGAEVGCQGEVGVACSMAAAGLAAALGGTNA 367
                                           *************987.567899************************************************** PP

                             TIGR00720 363 qvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmk 435
                                           q+enaaei+mehnlGltCdP+gGlvqiPCierna++a+kai+aarlal +dg++ vsldkvi+tm+ tG+dm+
  lcl|FitnessBrowser__Caulo:CCNA_03206 368 QIENAAEIGMEHNLGLTCDPIGGLVQIPCIERNAMGAIKAIDAARLALLGDGQHSVSLDKVIATMKRTGEDMN 440
                                           ************************************************************************* PP

                             TIGR00720 436 akyketskgGlav 448
                                           + ykets gGlav
  lcl|FitnessBrowser__Caulo:CCNA_03206 441 EIYKETSMGGLAV 453
                                           ************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (462 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.74
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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