Alignments for a candidate for sdaB in Dyadobacter tibetensis Y620-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Dyadobacter tibetensis Y620-1

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_025762082.1 X939_RS0104550 L-serine ammonia-lyase

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



>NCBI__GCF_000566685.1:WP_025762082.1
          Length = 474

 Score =  444 bits (1142), Expect = e-129
 Identities = 244/467 (52%), Positives = 310/467 (66%), Gaps = 19/467 (4%)

Query: 3   LSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKGHG 62
           +SVFD+FKIG+GPSSSHT+GP RAA +F + L + D L    S++V LYGSL  TG GHG
Sbjct: 6   ISVFDIFKIGVGPSSSHTLGPWRAAEKFLDELDQKDWLTEVKSIQVLLYGSLAKTGIGHG 65

Query: 63  SDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMI-RKPLA 121
           +D+AV LGL G  P  +D + +   +  I+    L L G H I F+ K  +  + ++ LA
Sbjct: 66  TDQAVALGLSGHDPILIDCQQIGTYISEIKEQKHLELKGMHRIPFDYKNDIVFLFKESLA 125

Query: 122 FHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLTFPFKSAKDLL 181
           FHPN + FR   A G     R Y+S+GGGFV+ E     + I      L +P  +  DLL
Sbjct: 126 FHPNALRFRVNLANGA-THERVYFSIGGGFVIQEHE---EVITSPDFQLPYPVDTGSDLL 181

Query: 182 GHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVKR 241
            HC    LSI ++++ NE  WR E E RAGLL IW+VM + + AGCRN GILPGGL+VKR
Sbjct: 182 SHCKGSQLSIWELVMANECCWREEQEVRAGLLHIWKVMTESIFAGCRNSGILPGGLQVKR 241

Query: 242 RAAALHRQLC-KNPEAALRDPLSV-----------LDWVNLYALAVNEENAYGGRVVTAP 289
           RAAAL  +L  + P       LS+           LDWVN +ALAVNEENA   RVVTAP
Sbjct: 242 RAAALSNKLLHQKPAQDYEQWLSLITQEGNGFHYTLDWVNCFALAVNEENASFSRVVTAP 301

Query: 290 TNGAAGIIPAVLHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGV 349
           TNGAAG+IPAVL YYM F  G  E  VV+FLLTA  IG ++K+ A+IS A  GCQ E+GV
Sbjct: 302 TNGAAGVIPAVLQYYMIFCEG-DEASVVKFLLTAGVIGSIFKKGATISAAMGGCQAEIGV 360

Query: 350 ACSMAAGALCEVLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAIN 409
           + +MAA  L +VLGGSV+Q   AAEI MEH+LGLTCDPIGGLVQ+PCIERN MG++KAI 
Sbjct: 361 SSAMAAAGLTQVLGGSVEQCMEAAEIAMEHHLGLTCDPIGGLVQIPCIERNTMGAIKAIT 420

Query: 410 AVRMAMRGD-GHHFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNI 455
           A ++A++G+ G   VSLD V++TM +T  DM  +YKET+ GGLA+ I
Sbjct: 421 ASQLALQGEPGDAKVSLDHVVQTMWETAQDMHHRYKETSEGGLALRI 467


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: 634
Number of extensions: 25
Number of successful extensions: 7
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: 474
Length adjustment: 33
Effective length of query: 425
Effective length of database: 441
Effective search space:   187425
Effective search space used:   187425
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_025762082.1 X939_RS0104550 (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.266838.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-182  591.9   0.0   6.7e-182  591.3   0.0    1.3  1  NCBI__GCF_000566685.1:WP_025762082.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000566685.1:WP_025762082.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  591.3   0.0  6.7e-182  6.7e-182       1     449 [.       6     466 ..       6     467 .. 0.94

  Alignments for each domain:
  == domain 1  score: 591.3 bits;  conditional E-value: 6.7e-182
                             TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGel 73 
                                           isvfd+fkiG+GPsssht+GP +aa++f++el++k+ l++vk+++v lyGsla tG Gh+td+av lGl G++
  NCBI__GCF_000566685.1:WP_025762082.1   6 ISVFDIFKIGVGPSSSHTLGPWRAAEKFLDELDQKDWLTEVKSIQVLLYGSLAKTGIGHGTDQAVALGLSGHD 78 
                                           79*********************************************************************** PP

                             TIGR00720  74 peevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevlkektyysv 145
                                           p  +d ++i + ++e++e+k+l+l++ ++i fd+++d++f  +e+l +h+n+lr+++   +    +e++y+s+
  NCBI__GCF_000566685.1:WP_025762082.1  79 PILIDCQQIGTYISEIKEQKHLELKGMHRIPFDYKNDIVFLfKESLAFHPNALRFRVNLAN-GATHERVYFSI 150
                                           ****************************************99*************987777.6789******* PP

                             TIGR00720 146 GGGfivdeeelkkeeeeeeevpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeec 218
                                           GGGf+++e+e +  ++ + ++pyp  + ++ll++Ck ++lsi e+v++ne+++r+e+evra ll+iwkvm+e+
  NCBI__GCF_000566685.1:WP_025762082.1 151 GGGFVIQEHE-EVITSPDFQLPYPVDTGSDLLSHCKGSQLSIWELVMANECCWREEQEVRAGLLHIWKVMTES 222
                                           ******9866.55667788****************************************************** PP

                             TIGR00720 219 ierglkaegvlpGglkvkrraaslkrklkakeets.............kdplavldwvnlyalavneenaaGg 278
                                           i  g+++ g+lpGgl+vkrraa+l +kl +++ ++             +    +ldwvn +alavneena+  
  NCBI__GCF_000566685.1:WP_025762082.1 223 IFAGCRNSGILPGGLQVKRRAAALSNKLLHQKPAQdyeqwlslitqegNGFHYTLDWVNCFALAVNEENASFS 295
                                           ****************************998876533222222111112334579****************** PP

                             TIGR00720 279 rvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaa 351
                                           rvvtaPtnGaag+iPavl+yy  f+e   e +vv+flltag+iG+++k+ a+is+a  GCq+e+Gv+++maaa
  NCBI__GCF_000566685.1:WP_025762082.1 296 RVVTAPTNGAAGVIPAVLQYYMIFCEGD-EASVVKFLLTAGVIGSIFKKGATISAAMGGCQAEIGVSSAMAAA 367
                                           ************************9976.67899*************************************** PP

                             TIGR00720 352 glaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedg.kkkvsldkv 423
                                           gl+++lgg++eq ++aaeiameh+lGltCdP+gGlvqiPCiern+++a+kai a++lal+++  + kvsld+v
  NCBI__GCF_000566685.1:WP_025762082.1 368 GLTQVLGGSVEQCMEAAEIAMEHHLGLTCDPIGGLVQIPCIERNTMGAIKAITASQLALQGEPgDAKVSLDHV 440
                                           ************************************************************98669******** PP

                             TIGR00720 424 ietmretGkdmkakyketskgGlavk 449
                                           ++tm et +dm+++ykets+gGla +
  NCBI__GCF_000566685.1:WP_025762082.1 441 VQTMWETAQDMHHRYKETSEGGLALR 466
                                           ************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (474 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 27.44
//
[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)
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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 2024 update 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