Alignments for a candidate for sdaB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Pedobacter sp. GW460-11-11-14-LB5

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate CA265_RS21785 CA265_RS21785 L-serine ammonia-lyase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5557
         (458 letters)



>FitnessBrowser__Pedo557:CA265_RS21785
          Length = 475

 Score =  438 bits (1126), Expect = e-127
 Identities = 238/467 (50%), Positives = 314/467 (67%), Gaps = 18/467 (3%)

Query: 3   LSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKGHG 62
           +SVFD+FKIGIGPSSSHT+GP RAA +F   L ++ L++    +K+ LYGSL  TGKGHG
Sbjct: 6   ISVFDIFKIGIGPSSSHTLGPWRAAQQFTASLAQNHLIDEIEGIKILLYGSLAKTGKGHG 65

Query: 63  SDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFN-EKLHLAMIRKPLA 121
           +D A+LLGL G  P T D + V    ++I+   +LNL G   I+F+ +   L +  + L 
Sbjct: 66  TDVAILLGLTGADPVTFDVDAVTPTFESIQRDQKLNLAGHLIIDFDYDNDLLFLFAESLP 125

Query: 122 FHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLTFPFKSAKDLL 181
           FHPN + F+AF   G +  S  YYS+GGGFVV EG    D   +    L FP + AKDLL
Sbjct: 126 FHPNAVTFQAFLKGG-KAFSETYYSIGGGFVVKEGE---DNSKKPQVDLPFPVEKAKDLL 181

Query: 182 GHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVKR 241
             C + GL +S++++ NE AWR EAET+ G+L+ + VM DC+  GC   G LPGGL V R
Sbjct: 182 HWCLSTGLKVSEIVMENELAWRTEAETKKGILQHFAVMSDCIYRGCHTTGFLPGGLNVAR 241

Query: 242 RAAALHRQLCKNPE--------AALRDPLS----VLDWVNLYALAVNEENAYGGRVVTAP 289
           RA  L+++L    E         A+R   +     LDWV+ +ALAVNEENA  GRVVTAP
Sbjct: 242 RAFPLNKRLIGKSEYSDYNSWVEAIRKGGNGFNYTLDWVSCFALAVNEENASFGRVVTAP 301

Query: 290 TNGAAGIIPAVLHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGV 349
           TNGAAG+IPAVL Y++ F  G SE+ +++F+  A+ IG ++K+ A+IS A  GCQ E+GV
Sbjct: 302 TNGAAGVIPAVLQYFITFCDGYSEEKIMQFIACASEIGSIFKKGATISAAMGGCQAEIGV 361

Query: 350 ACSMAAGALCEVLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAIN 409
           + +MAA AL E LGGS +QV  AAEI MEH+LGLTCDPIGGLVQ+PCIERN MG++KAI 
Sbjct: 362 SSAMAAAALTECLGGSQRQVLMAAEIAMEHHLGLTCDPIGGLVQIPCIERNTMGAIKAIT 421

Query: 410 AVRMAMRGDGHHF-VSLDKVIRTMRQTGADMKSKYKETARGGLAVNI 455
           A ++A++ +     VSLD V+ TM +T  DM +KYKET+ GGLA NI
Sbjct: 422 ASQLALQSNPDKAKVSLDAVVNTMWETALDMNAKYKETSDGGLATNI 468


Lambda     K      H
   0.320    0.136    0.401 

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: 593
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: 458
Length of database: 475
Length adjustment: 33
Effective length of query: 425
Effective length of database: 442
Effective search space:   187850
Effective search space used:   187850
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 CA265_RS21785 CA265_RS21785 (L-serine ammonia-lyase)
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.27522.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   5.1e-180  585.1   0.0     7e-180  584.7   0.0    1.2  1  lcl|FitnessBrowser__Pedo557:CA265_RS21785  CA265_RS21785 L-serine ammonia-l


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS21785  CA265_RS21785 L-serine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  584.7   0.0    7e-180    7e-180       1     450 []       6     468 ..       6     468 .. 0.95

  Alignments for each domain:
  == domain 1  score: 584.7 bits;  conditional E-value: 7e-180
                                  TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllG 68 
                                                isvfd+fkiGiGPsssht+GP +aa++f ++l ++  +++++ +k+ lyGsla tGkGh+td a+llG
  lcl|FitnessBrowser__Pedo557:CA265_RS21785   6 ISVFDIFKIGIGPSSSHTLGPWRAAQQFTASLAQNHLIDEIEGIKILLYGSLAKTGKGHGTDVAILLG 73 
                                                79****************************************************************** PP

                                  TIGR00720  69 leGelpeevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeege 135
                                                l+G +p + d++ ++  +e++++++kl+la++  i+fd+++dl f   e+lp+h+n+++++a+ + g+
  lcl|FitnessBrowser__Pedo557:CA265_RS21785  74 LTGADPVTFDVDAVTPTFESIQRDQKLNLAGHLIIDFDYDNDLLFLfAESLPFHPNAVTFQAFLKGGK 141
                                                *********************************************99****************99965 PP

                                  TIGR00720 136 vlkektyysvGGGfivdeeelkkeeeeeeevpypfksaaellelCkeeglsisevvlenekalrseee 203
                                                   ++tyys+GGGf+v+e e +++++ ++++p+p + a++ll+ C ++gl++se+v+ene a+r+e+e
  lcl|FitnessBrowser__Pedo557:CA265_RS21785 142 -AFSETYYSIGGGFVVKEGE-DNSKKPQVDLPFPVEKAKDLLHWCLSTGLKVSEIVMENELAWRTEAE 207
                                                .5689***********9876.56678889*************************************** PP

                                  TIGR00720 204 vraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets.............kdpla 258
                                                +++ +l+ + vm++ci rg+++ g+lpGgl+v rra  l+++l  k+e s             +    
  lcl|FitnessBrowser__Pedo557:CA265_RS21785 208 TKKGILQHFAVMSDCIYRGCHTTGFLPGGLNVARRAFPLNKRLIGKSEYSdynswveairkggNGFNY 275
                                                *******************************************9877765442222111111122345 PP

                                  TIGR00720 259 vldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilyk 326
                                                +ldwv+ +alavneena+ grvvtaPtnGaag+iPavl+y+ +f++  seek+++f+  a+ iG+++k
  lcl|FitnessBrowser__Pedo557:CA265_RS21785 276 TLDWVSCFALAVNEENASFGRVVTAPTNGAAGVIPAVLQYFITFCDGYSEEKIMQFIACASEIGSIFK 343
                                                79****************************************************************** PP

                                  TIGR00720 327 enasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCier 394
                                                + a+is+a  GCq+e+Gv+++maaa+l+e lgg+++qv +aaeiameh+lGltCdP+gGlvqiPCier
  lcl|FitnessBrowser__Pedo557:CA265_RS21785 344 KGATISAAMGGCQAEIGVSSAMAAAALTECLGGSQRQVLMAAEIAMEHHLGLTCDPIGGLVQIPCIER 411
                                                ******************************************************************** PP

                                  TIGR00720 395 naiaavkainaarlalkedg.kkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                                n+++a+kai a++lal+++  k kvsld v++tm et  dm+akykets gGla+++
  lcl|FitnessBrowser__Pedo557:CA265_RS21785 412 NTMGAIKAITASQLALQSNPdKAKVSLDAVVNTMWETALDMNAKYKETSDGGLATNI 468
                                                *****************997589*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (475 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.36
//
[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