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.26788.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.39
//
[ok]

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

Links

Downloads

Related tools

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:

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:

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:

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:

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