Alignments for a candidate for hutH in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Bacteroides thetaiotaomicron VPI-5482

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate 352217 BT2690 histidine ammonia-lyase (NCBI ptt file)

Query= reanno::SB2B:6937475
         (497 letters)



>FitnessBrowser__Btheta:352217
          Length = 499

 Score =  405 bits (1042), Expect = e-117
 Identities = 224/490 (45%), Positives = 312/490 (63%), Gaps = 4/490 (0%)

Query: 3   FRYGVDHLTLETVNGIANGSIQAELCQQAIDKINASRHNVD-VMAASDKAIYGINTGFGP 61
           ++ G   LT E +  I N +++ EL  +A  +I   R  +D  +A+S++ +YGI TGFG 
Sbjct: 6   YQIGSGELTFEIIERIINENLKLELAPEAKLRIQKCRDYLDHKIASSEEPLYGITTGFGS 65

Query: 62  LCDTQISPAETHLLQKNLLITHAVGVGEPIAKSISKLMLITKVHALSQGFSGIRLDVVER 121
           LC   ISP E   LQ+NL+ +HA  VGE I   I KLM++ K HALS G SG++L  V+R
Sbjct: 66  LCTKNISPGELGTLQENLIKSHACSVGEEIRPVIIKLMMLLKAHALSLGHSGVQLITVQR 125

Query: 122 MLAFIALDLIPVVPEQGSVGASGDLAPLSHLFLPLLGEGEFWQGDKIVPAREALKAHGLE 181
           +L F   D++P+V ++GS+GASGDLAPL++LFLPL+G G+     K   A   L   G E
Sbjct: 126 ILDFFNNDVLPIVYDRGSLGASGDLAPLANLFLPLIGVGDVNYKGKKCEAISVLDEFGWE 185

Query: 182 PLELHAKEGLALINGTQFILSHAITALTKMGYLLDLADLAGAMSIEGMQGSQSPFRAELH 241
           P+ L +KEGLAL+NGTQF+ ++ + A+ K   L   ADL  A+S+E   G   PF   + 
Sbjct: 186 PVRLMSKEGLALLNGTQFMSANGVFAILKAFRLSKKADLIAALSLEAFDGRIDPFMDCIQ 245

Query: 242 EIRPFAGNIEVAARMRSFFKDSENMASHEDCDRVQDPYSLRCIPQVHGASRNAYNHLKEL 301
           +IRP  G IE     R     SE +   +    VQDPYS RCIPQVHGA+++A  ++  +
Sbjct: 246 QIRPHPGQIETGEAFRKLLAGSELIERPK--AHVQDPYSFRCIPQVHGATKDAIRYVSSV 303

Query: 302 AEIEMNSVTDNPIVISAEE-AISGGGFHGQPLAMVLDYTSIAAAELGNISDRRCYLLLEG 360
              E+NSVTDNP +   E+  ISGG FHGQPLA+  D+ +IA AELGNIS+RR   L+ G
Sbjct: 304 LLTEINSVTDNPTIFPDEDRIISGGNFHGQPLAISYDFLAIALAELGNISERRVSQLIMG 363

Query: 361 LHGLPRLLTTSGGLNSGMMIPQYVTAALVTENKSLCFPPSADSVPTSMGQEDHVSMGSIS 420
           L  LP  L  + GLNSG MIPQY  A++V++NK  C+  S+DS+ +S GQEDHVSMG+ +
Sbjct: 364 LRELPEFLVANPGLNSGFMIPQYAAASMVSQNKMYCYAASSDSIVSSNGQEDHVSMGANA 423

Query: 421 GRKLNQILGNLEKIFAIELMYAAQAIDFRRPNRCSDIIEQNHALIREKVAKLEEDRLLKP 480
             KL +++ NLE I AIELM AAQ IDFRRP + S ++E      R++V  +++D ++  
Sbjct: 424 ATKLYKVMDNLEHILAIELMNAAQGIDFRRPLKTSPLLESFLHAYRKEVPFVKDDIVMYK 483

Query: 481 DIDAIIALVK 490
           +I   +A +K
Sbjct: 484 EIHKTVAFLK 493


Lambda     K      H
   0.319    0.136    0.387 

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: 586
Number of extensions: 25
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: 497
Length of database: 499
Length adjustment: 34
Effective length of query: 463
Effective length of database: 465
Effective search space:   215295
Effective search space used:   215295
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: 52 (24.6 bits)

Align candidate 352217 BT2690 (histidine ammonia-lyase (NCBI ptt file))
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.8933.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     1e-177  577.5   0.0   1.2e-177  577.4   0.0    1.0  1  lcl|FitnessBrowser__Btheta:352217  BT2690 histidine ammonia-lyase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:352217  BT2690 histidine ammonia-lyase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  577.4   0.0  1.2e-177  1.2e-177       3     494 ..       8     497 ..       6     499 .] 0.98

  Alignments for each domain:
  == domain 1  score: 577.4 bits;  conditional E-value: 1.2e-177
                          TIGR01225   3 ldgesltledleavarekarvelsaaaeeavaksravie.eivaedktvYGvntGFGklasvkidkedlaeLqrnl 77 
                                        + +++lt e +e++  e+ ++el+ +a+ +++k r  ++ +i+++++++YG++tGFG+l   +i   +l +Lq+nl
  lcl|FitnessBrowser__Btheta:352217   8 IGSGELTFEIIERIINENLKLELAPEAKLRIQKCRDYLDhKIASSEEPLYGITTGFGSLCTKNISPGELGTLQENL 83 
                                        667899*******************************983688899****************************** PP

                          TIGR01225  78 vrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLahlalv 153
                                        ++sHa+ vGe++   +++++++l++++l+ G+sgv+  +++ +++++n++vlP+v ++Gs+GasGDLAPLa l l 
  lcl|FitnessBrowser__Btheta:352217  84 IKSHACSVGEEIRPVIIKLMMLLKAHALSLGHSGVQLITVQRILDFFNNDVLPIVYDRGSLGASGDLAPLANLFLP 159
                                        **************************************************************************** PP

                          TIGR01225 154 liGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalsleallg 229
                                        liG G+++++g+  +a ++L++ g ePv+l +kEGlAL+nGtq+m+a +v a+ +a +l ++ad++aalslea  g
  lcl|FitnessBrowser__Btheta:352217 160 LIGVGDVNYKGKKCEAISVLDEFGWEPVRLMSKEGLALLNGTQFMSANGVFAILKAFRLSKKADLIAALSLEAFDG 235
                                        **************************************************************************** PP

                          TIGR01225 230 tskafdpdihevrphrgqiavaarlrellagseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiEln 305
                                          ++f + i+++rph+gqi++++++r+llagse+ e+   + +vqD+Ys RciPqvhGa++d++++v +vl +E+n
  lcl|FitnessBrowser__Btheta:352217 236 RIDPFMDCIQQIRPHPGQIETGEAFRKLLAGSELIERP--KAHVQDPYSFRCIPQVHGATKDAIRYVSSVLLTEIN 309
                                        ***********************************998..899********************************* PP

                          TIGR01225 306 satDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmia 381
                                        s+tDnP +f+de++++sgGnFHg+p+A+  dflaia+aelg+iseRR+++l+   l eLp FL++++GlnsG+mi+
  lcl|FitnessBrowser__Btheta:352217 310 SVTDNPTIFPDEDRIISGGNFHGQPLAISYDFLAIALAELGNISERRVSQLIM-GLRELPEFLVANPGLNSGFMIP 384
                                        ***************************************************96.6889****************** PP

                          TIGR01225 382 qytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrkaektaae 457
                                        qy+aA++vs+nk  ++ as Dsi +s  qEDHvsmga aa kl++v++n+++++aiEl+ aaqg++fr++ kt++ 
  lcl|FitnessBrowser__Btheta:352217 385 QYAAASMVSQNKMYCYAASSDSIVSSNGQEDHVSMGANAATKLYKVMDNLEHILAIELMNAAQGIDFRRPLKTSPL 460
                                        **************************************************************************** PP

                          TIGR01225 458 lekvyeavRevveeleeDRvlapDleavkellekesl 494
                                        le   +a R++v+ +++D v+ +++++   +l++ +l
  lcl|FitnessBrowser__Btheta:352217 461 LESFLHAYRKEVPFVKDDIVMYKEIHKTVAFLKRTKL 497
                                        *****************************99998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (499 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: 9.16
//
[ok]

This GapMind analysis is from Sep 17 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)
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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