Alignments for a candidate for sdaB in Methylohalobius crimeensis 10Ki

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Methylohalobius crimeensis 10Ki

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_022948746.1 H035_RS0109505 L-serine ammonia-lyase

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



>NCBI__GCF_000421465.1:WP_022948746.1
          Length = 460

 Score =  590 bits (1522), Expect = e-173
 Identities = 309/462 (66%), Positives = 355/462 (76%), Gaps = 6/462 (1%)

Query: 1   MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKG 60
           M +S+FDLFKIGIGPSSSHTVGPMRAA +FA  L    L     S+ ++LYGSL  TG+G
Sbjct: 1   MHISIFDLFKIGIGPSSSHTVGPMRAAYQFAGSLSEAGLTGRLASLTIDLYGSLADTGRG 60

Query: 61  HGSDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMIR-KP 119
           HG+DKAVLLGLEGE P++VD ET+D R+  IR    L L G   I F++   L   R K 
Sbjct: 61  HGTDKAVLLGLEGEMPESVDPETIDGRIAVIRKKRLLRLRGAKEIPFDDSKQLIFHRGKQ 120

Query: 120 LAFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEG--AAGADRIVEDATPLTFPFKSA 177
           L FHPNGM   A+DA G ++R+ E+YSVGGGFVV+E   A G      D  P  F  +SA
Sbjct: 121 LPFHPNGMRCTAWDADGREIRAEEFYSVGGGFVVNEKMLAEGFPDRAGDQAPCAF--RSA 178

Query: 178 KDLLGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGL 237
           +DLL  C T   ++S ++L +E  WR +AE   GL  IW  MQ+CV  GCR +GILPGG+
Sbjct: 179 RDLLELCRTRNCAVSDILLAHEKTWRSQAEIENGLRHIWYTMQECVEKGCRRDGILPGGM 238

Query: 238 KVKRRAAALHRQL-CKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGI 296
           K+KRRA A++RQL   + + A   PL  LDWVNL+ALAV+EENA GGRVVTAPTNGAAGI
Sbjct: 239 KIKRRAPAIYRQLQSSDAQLASAAPLGTLDWVNLFALAVSEENAAGGRVVTAPTNGAAGI 298

Query: 297 IPAVLHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAG 356
           IPAVLHYY RF  GA+E GV+RFLLTAAAI +LYK NASISGAEVGCQGEVGVA SMAAG
Sbjct: 299 IPAVLHYYTRFCSGANEAGVIRFLLTAAAIAMLYKMNASISGAEVGCQGEVGVASSMAAG 358

Query: 357 ALCEVLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAMR 416
           AL EVLGGS  QVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMG+VKAINA R+A+R
Sbjct: 359 ALTEVLGGSPAQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGAVKAINASRIALR 418

Query: 417 GDGHHFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458
           GDG HFVSLDKVI+TMRQTGADMKSKYKETARGGLAVN+IEC
Sbjct: 419 GDGSHFVSLDKVIKTMRQTGADMKSKYKETARGGLAVNVIEC 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: 702
Number of extensions: 26
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: 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_022948746.1 H035_RS0109505 (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.4082.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-212  692.8   0.0   1.2e-212  692.6   0.0    1.0  1  lcl|NCBI__GCF_000421465.1:WP_022948746.1  H035_RS0109505 L-serine ammonia-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000421465.1:WP_022948746.1  H035_RS0109505 L-serine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  692.6   0.0  1.2e-212  1.2e-212       1     450 []       3     457 ..       3     457 .. 0.98

  Alignments for each domain:
  == domain 1  score: 692.6 bits;  conditional E-value: 1.2e-212
                                 TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGl 69 
                                               is+fdlfkiGiGPssshtvGPm+aa++f+ +l+++g   +++++++dlyGsla tG+Gh+tdkavllGl
  lcl|NCBI__GCF_000421465.1:WP_022948746.1   3 ISIFDLFKIGIGPSSSHTVGPMRAAYQFAGSLSEAGLTGRLASLTIDLYGSLADTGRGHGTDKAVLLGL 71 
                                               79******************************************************************* PP

                                 TIGR00720  70 eGelpeevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevl 137
                                               eGe+pe+vd e+i+ +++ +++++ l+l + kei fd +k+l+f+  ++lp+h+ng+r +a+d +g+ +
  lcl|NCBI__GCF_000421465.1:WP_022948746.1  72 EGEMPESVDPETIDGRIAVIRKKRLLRLRGAKEIPFDDSKQLIFHrGKQLPFHPNGMRCTAWDADGREI 140
                                               *********************************************889********************* PP

                                 TIGR00720 138 kektyysvGGGfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekalrseeev 204
                                               +++++ysvGGGf+v+e+ l +   +++  ++p +f+sa++llelC++++ ++s+++l+ ek++rs++e+
  lcl|NCBI__GCF_000421465.1:WP_022948746.1 141 RAEEFYSVGGGFVVNEKMLAEGFPDRAgdQAPCAFRSARDLLELCRTRNCAVSDILLAHEKTWRSQAEI 209
                                               ******************99987776667**************************************** PP

                                 TIGR00720 205 raklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets..kdplavldwvnlyalavn 271
                                               ++ l +iw +m+ec+e+g++++g+lpGg+k+krra++++r+l++++ +   ++pl +ldwvnl+alav+
  lcl|NCBI__GCF_000421465.1:WP_022948746.1 210 ENGLRHIWYTMQECVEKGCRRDGILPGGMKIKRRAPAIYRQLQSSDAQLasAAPLGTLDWVNLFALAVS 278
                                               *******************************************9987644599**************** PP

                                 TIGR00720 272 eenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqg 340
                                               eenaaGgrvvtaPtnGaagiiPavl+yy++f++ a+e  v+rfllta+ai +lyk+nasisgaevGCqg
  lcl|NCBI__GCF_000421465.1:WP_022948746.1 279 EENAAGGRVVTAPTNGAAGIIPAVLHYYTRFCSGANEAGVIRFLLTAAAIAMLYKMNASISGAEVGCQG 347
                                               ********************************************************************* PP

                                 TIGR00720 341 evGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarla 409
                                               evGva+smaa++l+e+lgg+p qvenaaei+mehnlGltCdP+gGlvq+PCierna++avkaina+r+a
  lcl|NCBI__GCF_000421465.1:WP_022948746.1 348 EVGVASSMAAGALTEVLGGSPAQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGAVKAINASRIA 416
                                               ********************************************************************* PP

                                 TIGR00720 410 lkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                               l++dg+++vsldkvi+tmr+tG+dmk+kyket++gGlav+v
  lcl|NCBI__GCF_000421465.1:WP_022948746.1 417 LRGDGSHFVSLDKVIKTMRQTGADMKSKYKETARGGLAVNV 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: 9.99
//
[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)
Rules (tab-delimited)
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