Alignments for a candidate for hutH in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Phaeobacter inhibens BS107

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate GFF3579 PGA1_c36340 histidine ammonia-lyase HutH

Query= reanno::Phaeo:GFF3579
         (507 letters)



>FitnessBrowser__Phaeo:GFF3579
          Length = 507

 Score =  979 bits (2531), Expect = 0.0
 Identities = 507/507 (100%), Positives = 507/507 (100%)

Query: 1   MIEMIPGTVTLSTLEDIYRNLTPAKLASSAREPVEAAAQMVAEAAAGQEAVYGINTGFGK 60
           MIEMIPGTVTLSTLEDIYRNLTPAKLASSAREPVEAAAQMVAEAAAGQEAVYGINTGFGK
Sbjct: 1   MIEMIPGTVTLSTLEDIYRNLTPAKLASSAREPVEAAAQMVAEAAAGQEAVYGINTGFGK 60

Query: 61  LASTKIAPEDTATLQRNLILSHCCGVGEALPEDKTRLMMTLKLLSMGRGASGVRWLVIDQ 120
           LASTKIAPEDTATLQRNLILSHCCGVGEALPEDKTRLMMTLKLLSMGRGASGVRWLVIDQ
Sbjct: 61  LASTKIAPEDTATLQRNLILSHCCGVGEALPEDKTRLMMTLKLLSMGRGASGVRWLVIDQ 120

Query: 121 IEKMLAHGVIPVIPSQGSVGASGDLAPLAHMAAAMIGAGEATYDGTRMSSAEALKKAGLE 180
           IEKMLAHGVIPVIPSQGSVGASGDLAPLAHMAAAMIGAGEATYDGTRMSSAEALKKAGLE
Sbjct: 121 IEKMLAHGVIPVIPSQGSVGASGDLAPLAHMAAAMIGAGEATYDGTRMSSAEALKKAGLE 180

Query: 181 PIVLGPKEGLGLINGTQFSTACALAGLFDAWRMAEASMTIASLSTDAIMGSTAPLIADIH 240
           PIVLGPKEGLGLINGTQFSTACALAGLFDAWRMAEASMTIASLSTDAIMGSTAPLIADIH
Sbjct: 181 PIVLGPKEGLGLINGTQFSTACALAGLFDAWRMAEASMTIASLSTDAIMGSTAPLIADIH 240

Query: 241 TLRGHAGQINVAQQMREIMDGSEIRESHREGDTRVQDPYCIRCQPQVVGAALDVLRMAAK 300
           TLRGHAGQINVAQQMREIMDGSEIRESHREGDTRVQDPYCIRCQPQVVGAALDVLRMAAK
Sbjct: 241 TLRGHAGQINVAQQMREIMDGSEIRESHREGDTRVQDPYCIRCQPQVVGAALDVLRMAAK 300

Query: 301 TLEIEANAVTDNPLVLVNEGRIVSGGNFHAEYVGFAADQIALAVAEIGAIAQRRVALMVD 360
           TLEIEANAVTDNPLVLVNEGRIVSGGNFHAEYVGFAADQIALAVAEIGAIAQRRVALMVD
Sbjct: 301 TLEIEANAVTDNPLVLVNEGRIVSGGNFHAEYVGFAADQIALAVAEIGAIAQRRVALMVD 360

Query: 361 PTLSHDLPPFLTPDPGLNSGFMIAEVTTAALMSENKHLANPCVTDSTPTSANQEDHVSMA 420
           PTLSHDLPPFLTPDPGLNSGFMIAEVTTAALMSENKHLANPCVTDSTPTSANQEDHVSMA
Sbjct: 361 PTLSHDLPPFLTPDPGLNSGFMIAEVTTAALMSENKHLANPCVTDSTPTSANQEDHVSMA 420

Query: 421 AHGALRLARMNANLSVILGVEMLCAAQGVEARAPLQTSARLQDVLGMLRADIPALAEDRY 480
           AHGALRLARMNANLSVILGVEMLCAAQGVEARAPLQTSARLQDVLGMLRADIPALAEDRY
Sbjct: 421 AHGALRLARMNANLSVILGVEMLCAAQGVEARAPLQTSARLQDVLGMLRADIPALAEDRY 480

Query: 481 LAPDIEDASAMVRAGRVAEAAGVKVTA 507
           LAPDIEDASAMVRAGRVAEAAGVKVTA
Sbjct: 481 LAPDIEDASAMVRAGRVAEAAGVKVTA 507


Lambda     K      H
   0.317    0.131    0.368 

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: 912
Number of extensions: 18
Number of successful extensions: 1
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: 507
Length of database: 507
Length adjustment: 34
Effective length of query: 473
Effective length of database: 473
Effective search space:   223729
Effective search space used:   223729
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate GFF3579 PGA1_c36340 (histidine ammonia-lyase HutH)
to HMM TIGR01225 (hutH: histidine ammonia-lyase (EC 4.3.1.3))

# 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/TIGR01225.hmm
# target sequence database:        /tmp/gapView.4497.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01225  [M=506]
Accession:   TIGR01225
Description: hutH: histidine 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   9.3e-204  663.4  11.0     1e-203  663.3  11.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3579  PGA1_c36340 histidine ammonia-ly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3579  PGA1_c36340 histidine ammonia-lyase HutH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  663.3  11.0    1e-203    1e-203       3     501 ..       4     504 ..       2     507 .] 0.99

  Alignments for each domain:
  == domain 1  score: 663.3 bits;  conditional E-value: 1e-203
                          TIGR01225   3 ldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeLqrnlv 78 
                                        + ++++tl+ le ++r+ ++++l+ +a+e v++++++++e +a++++vYG+ntGFGklas+ki+ ed+a+Lqrnl+
  lcl|FitnessBrowser__Phaeo:GFF3579   4 MIPGTVTLSTLEDIYRNLTPAKLASSAREPVEAAAQMVAEAAAGQEAVYGINTGFGKLASTKIAPEDTATLQRNLI 79 
                                        557799********************************************************************** PP

                          TIGR01225  79 rsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLahlalvl 154
                                        +sH++GvGe l+e+ +R+++ l+l s+ +G+sgvr  v++++ ++l ++v+Pv+p++GsvGasGDLAPLah+a+++
  lcl|FitnessBrowser__Phaeo:GFF3579  80 LSHCCGVGEALPEDKTRLMMTLKLLSMGRGASGVRWLVIDQIEKMLAHGVIPVIPSQGSVGASGDLAPLAHMAAAM 155
                                        **************************************************************************** PP

                          TIGR01225 155 iGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalsleallgt 230
                                        iG Gea+++g++m++aeaL++agleP+ l  kEGl LinGtq++ta a+++l+da +++e++ ++a+ls++a++g+
  lcl|FitnessBrowser__Phaeo:GFF3579 156 IGAGEATYDGTRMSSAEALKKAGLEPIVLGPKEGLGLINGTQFSTACALAGLFDAWRMAEASMTIASLSTDAIMGS 231
                                        **************************************************************************** PP

                          TIGR01225 231 skafdpdihevrphrgqiavaarlrellagseiaeshk.dedrvqDaYslRciPqvhGavldtldqvkevlaiEln 305
                                        ++++ +dih++r+h gqi+va+++re+++gsei+esh+ +++rvqD+Y++Rc+Pqv Ga+ld+l++++++l+iE+n
  lcl|FitnessBrowser__Phaeo:GFF3579 232 TAPLIADIHTLRGHAGQINVAQQMREIMDGSEIRESHReGDTRVQDPYCIRCQPQVVGAALDVLRMAAKTLEIEAN 307
                                        **************************************99************************************ PP

                          TIGR01225 306 satDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpals.eLppFLaedsGlnsGlmi 380
                                        ++tDnPlv+ +eg++vsgGnFH+e+v +a+d++a+a+ae+gai++RR+++++dp+ls +LppFL++d+GlnsG+mi
  lcl|FitnessBrowser__Phaeo:GFF3579 308 AVTDNPLVLVNEGRIVSGGNFHAEYVGFAADQIALAVAEIGAIAQRRVALMVDPTLShDLPPFLTPDPGLNSGFMI 383
                                        *********************************************************9****************** PP

                          TIGR01225 381 aqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrkaektaa 456
                                        a++t+AaL+senk+La+P   Ds+ptsanqEDHvsm+a++a +l ++ +n++ ++++E+l+aaqg+e r++ +t+a
  lcl|FitnessBrowser__Phaeo:GFF3579 384 AEVTTAALMSENKHLANPCVTDSTPTSANQEDHVSMAAHGALRLARMNANLSVILGVEMLCAAQGVEARAPLQTSA 459
                                        **************************************************************************** PP

                          TIGR01225 457 elekvyeavRevveeleeDRvlapDleavkellekesleaaveak 501
                                        +l+ v  ++R+  + l+eDR+lapD+e ++ +++++++++a+  k
  lcl|FitnessBrowser__Phaeo:GFF3579 460 RLQDVLGMLRADIPALAEDRYLAPDIEDASAMVRAGRVAEAAGVK 504
                                        **************************************9998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (507 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: 11.25
//
[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