Alignments for a candidate for sdaB in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Stenotrophomonas chelatiphaga DSM 21508

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_057508715.1 ABB28_RS11230 L-serine ammonia-lyase

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



>NCBI__GCF_001431535.1:WP_057508715.1
          Length = 460

 Score =  612 bits (1578), Expect = e-180
 Identities = 307/460 (66%), Positives = 363/460 (78%), Gaps = 2/460 (0%)

Query: 1   MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDD-LLNCTTSVKVELYGSLGATGK 59
           M++S FD+FKIGIGPSSSHTVGPM+AA RF      D   L     ++ ++YGSL  TG+
Sbjct: 1   MAVSTFDVFKIGIGPSSSHTVGPMKAAERFVHRWLLDPGRLQDVVRIRADVYGSLALTGR 60

Query: 60  GHGSDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMI-RK 118
           GHG+DKAVLLGLEG+ P+ +D + + A L+ IR+S R+NL+G+H I F+EK  L +  R+
Sbjct: 61  GHGTDKAVLLGLEGQRPNLIDPDIIPATLERIRASKRINLMGQHEISFDEKRDLGLNKRQ 120

Query: 119 PLAFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLTFPFKSAK 178
            L +H NGM F A+ A    + +R+YYSVGGGFVV++  A  DRIV D TPL +PFKS  
Sbjct: 121 KLPYHTNGMRFTAYGANDELIATRDYYSVGGGFVVNQDDAADDRIVPDETPLPYPFKSGD 180

Query: 179 DLLGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLK 238
           +LL   +  GLSI+Q+M  NE +WR E + RA L +IW+ MQ CVA G R EG+LPGGLK
Sbjct: 181 ELLAQTARSGLSIAQLMFENEKSWRSEDDIRAQLREIWEAMQACVARGIRQEGVLPGGLK 240

Query: 239 VKRRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIIP 298
           V RRA ALHR+L   PEAA+RDPL+ LDWVNLYALAVNEENA GGRVVTAPTNGAAG++P
Sbjct: 241 VGRRAPALHRELSSKPEAAMRDPLTTLDWVNLYALAVNEENAAGGRVVTAPTNGAAGVLP 300

Query: 299 AVLHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGAL 358
           AVLHY+ RF PGA+E  +  FLLT+AAIGILYKENASISGAEVGCQGEVGVACSMAAG L
Sbjct: 301 AVLHYFDRFCPGANEQRIFDFLLTSAAIGILYKENASISGAEVGCQGEVGVACSMAAGGL 360

Query: 359 CEVLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAMRGD 418
              LGGS  Q+ENAAEIGMEHNLGLTCDPIGGLVQ+PCIERNAMG+VKAINA RMAMRGD
Sbjct: 361 VAALGGSPSQIENAAEIGMEHNLGLTCDPIGGLVQIPCIERNAMGAVKAINASRMAMRGD 420

Query: 419 GHHFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458
           G H VSLDKVI+TMR TG DM+ KYKET+RGGLAVN+IEC
Sbjct: 421 GKHKVSLDKVIKTMRDTGRDMQDKYKETSRGGLAVNVIEC 460


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: 697
Number of extensions: 30
Number of successful extensions: 3
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: 460
Length adjustment: 33
Effective length of query: 425
Effective length of database: 427
Effective search space:   181475
Effective search space used:   181475
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 WP_057508715.1 ABB28_RS11230 (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.6364.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     7e-220  716.5   0.0   7.9e-220  716.3   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057508715.1  ABB28_RS11230 L-serine ammonia-l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508715.1  ABB28_RS11230 L-serine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.3   0.0  7.9e-220  7.9e-220       1     450 []       3     457 ..       3     457 .. 0.98

  Alignments for each domain:
  == domain 1  score: 716.3 bits;  conditional E-value: 7.9e-220
                                 TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefvee.lkkkgkleqvkrvkvdlyGslaltGkGhktdkavllG 68 
                                               +s+fd+fkiGiGPssshtvGPmkaa++fv++ l + g+l++v r++ d+yGslaltG+Gh+tdkavllG
  lcl|NCBI__GCF_001431535.1:WP_057508715.1   3 VSTFDVFKIGIGPSSSHTVGPMKAAERFVHRwLLDPGRLQDVVRIRADVYGSLALTGRGHGTDKAVLLG 71 
                                               699**************************8747899********************************* PP

                                 TIGR00720  69 leGelpeevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegev 136
                                               leG+ p+ +d + i++ le+++++k+++l +q+ei+fd+++dl ++ +++lp+h ng+r++ay  ++e+
  lcl|NCBI__GCF_001431535.1:WP_057508715.1  72 LEGQRPNLIDPDIIPATLERIRASKRINLMGQHEISFDEKRDLGLNkRQKLPYHTNGMRFTAYGANDEL 140
                                               *********************************************9899******************** PP

                                 TIGR00720 137 lkektyysvGGGfivdeeelkkeee..eeeevpypfksaaellelCkeeglsisevvlenekalrseee 203
                                               ++++ yysvGGGf+v+++++ +++   +e+ +pypfks +ell++ +++glsi+++++enek++rse++
  lcl|NCBI__GCF_001431535.1:WP_057508715.1 141 IATRDYYSVGGGFVVNQDDAADDRIvpDETPLPYPFKSGDELLAQTARSGLSIAQLMFENEKSWRSEDD 209
                                               ****************9988776541145599************************************* PP

                                 TIGR00720 204 vraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets.kdplavldwvnlyalavn 271
                                               +ra+l eiw++m++c+ rg+++egvlpGglkv rra++l+r+l++k e+  +dpl++ldwvnlyalavn
  lcl|NCBI__GCF_001431535.1:WP_057508715.1 210 IRAQLREIWEAMQACVARGIRQEGVLPGGLKVGRRAPALHRELSSKPEAAmRDPLTTLDWVNLYALAVN 278
                                               **********************************************99988****************** PP

                                 TIGR00720 272 eenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqg 340
                                               eenaaGgrvvtaPtnGaag++Pavl+y+++f++ a+e+++ +fllt++aiGilykenasisgaevGCqg
  lcl|NCBI__GCF_001431535.1:WP_057508715.1 279 EENAAGGRVVTAPTNGAAGVLPAVLHYFDRFCPGANEQRIFDFLLTSAAIGILYKENASISGAEVGCQG 347
                                               ********************************************************************* PP

                                 TIGR00720 341 evGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarla 409
                                               evGvacsmaa+gl ++lgg+p+q+enaaei+mehnlGltCdP+gGlvqiPCierna++avkaina+r+a
  lcl|NCBI__GCF_001431535.1:WP_057508715.1 348 EVGVACSMAAGGLVAALGGSPSQIENAAEIGMEHNLGLTCDPIGGLVQIPCIERNAMGAVKAINASRMA 416
                                               ********************************************************************* PP

                                 TIGR00720 410 lkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                               +++dgk+kvsldkvi+tmr+tG+dm+ kykets+gGlav+v
  lcl|NCBI__GCF_001431535.1:WP_057508715.1 417 MRGDGKHKVSLDKVIKTMRDTGRDMQDKYKETSRGGLAVNV 457
                                               ***************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (460 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.05
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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