Alignments for a candidate for hutH in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Echinicola vietnamensis KMM 6221, DSM 17526

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate Echvi_0202 Echvi_0202 histidine ammonia-lyase

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



>FitnessBrowser__Cola:Echvi_0202
          Length = 508

 Score =  429 bits (1103), Expect = e-124
 Identities = 233/491 (47%), Positives = 321/491 (65%), Gaps = 5/491 (1%)

Query: 3   FRYGVDHLTLETVNGIANGSIQAELCQQAIDKINASRHNVDVMAASDKAI--YGINTGFG 60
           +R G   +TLE +  + +   + EL   AI++I   R  +D     D+A   YGINTGFG
Sbjct: 11  YRVGEMPVTLERIYRVVSEGKRLELSSAAIERIQQCRAYLDDKIYKDEAALYYGINTGFG 70

Query: 61  PLCDTQISPAETHLLQKNLLITHAVGVGEPIAKSISKLMLITKVHALSQGFSGIRLDVVE 120
            L   +I   E   LQ NLL +HA GVGE + K + +LML+TK+ +LS+G SG++L+ V+
Sbjct: 71  YLQQVRIDRNEIQQLQYNLLQSHACGVGEKVPKELVRLMLLTKIESLSRGHSGVQLETVQ 130

Query: 121 RMLAFIALDLIPVVPEQGSVGASGDLAPLSHLFLPLLGEGEFWQGDKIVPAREALKAHGL 180
           R++ F   D++PVV  QGS+GASGDL+PLSHL LPL+G GE +   K+ P+ + L+  G 
Sbjct: 131 RLVDFYNHDVLPVVYNQGSLGASGDLSPLSHLSLPLIGMGEVYFEGKVCPSAQVLEQFGW 190

Query: 181 EPLELHAKEGLALINGTQFILSHAITALTKMGYLLDLADLAGAMSIEGMQGSQSPFRAEL 240
           +P+ L +KEGL+LINGTQF+LS+ +    +   L   ADL  A+S++G  G+  PF A +
Sbjct: 191 QPVTLRSKEGLSLINGTQFMLSYGVHITQRAEALFRWADLIAAISVDGFNGNLQPFNALI 250

Query: 241 HEIRPFAGNIEVAARMRSFFKDSENMASHEDCDRVQDPYSLRCIPQVHGASRNAYNHLKE 300
           H IR   G ++ AA +R + + SE   S E   +VQDPYS RCIPQVHGAS++    +K 
Sbjct: 251 HRIRAHEGQVDTAASLRHYLEGSEIAQSKE--KQVQDPYSFRCIPQVHGASKDTLAFVKG 308

Query: 301 LAEIEMNSVTDNPIVISAE-EAISGGGFHGQPLAMVLDYTSIAAAELGNISDRRCYLLLE 359
             E E +SVTDNP +   E E +SGG FHGQPLA+  DY +IA AE+G+IS+RR Y LL 
Sbjct: 309 TFEREADSVTDNPNIFPDEDEILSGGNFHGQPLALAFDYLAIAMAEIGSISERRTYQLLS 368

Query: 360 GLHGLPRLLTTSGGLNSGMMIPQYVTAALVTENKSLCFPPSADSVPTSMGQEDHVSMGSI 419
           G  GLP  L    GL+SG+MIPQY  A++V+ENK LC P S DS+ +S GQEDHVSMG+ 
Sbjct: 369 GQRGLPLFLVDDPGLHSGLMIPQYTAASVVSENKQLCTPASVDSIVSSNGQEDHVSMGAN 428

Query: 420 SGRKLNQILGNLEKIFAIELMYAAQAIDFRRPNRCSDIIEQNHALIREKVAKLEEDRLLK 479
              K  ++L NLEKI AIEL+ AAQA++FRRP R S+I+E+   + R+ V+   +DR+L 
Sbjct: 429 GATKCLRVLDNLEKILAIELLTAAQALEFRRPARSSEIVERLIGVYRDHVSFNAQDRVLS 488

Query: 480 PDIDAIIALVK 490
            DI   I  ++
Sbjct: 489 VDIKNTIKFLR 499


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: 581
Number of extensions: 17
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: 497
Length of database: 508
Length adjustment: 34
Effective length of query: 463
Effective length of database: 474
Effective search space:   219462
Effective search space used:   219462
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 Echvi_0202 Echvi_0202 (histidine ammonia-lyase)
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.17359.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   8.4e-191  620.7   0.0   9.8e-191  620.5   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0202  Echvi_0202 histidine ammonia-lya


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0202  Echvi_0202 histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  620.5   0.0  9.8e-191  9.8e-191       7     495 ..      17     504 ..      12     508 .] 0.97

  Alignments for each domain:
  == domain 1  score: 620.5 bits;  conditional E-value: 9.8e-191
                            TIGR01225   7 sltledleavarekarvelsaaaeeavaksravieeivaedktv..YGvntGFGklasvkidkedlaeLqrnlv 78 
                                           +tle +++v+ e++r+els aa e++++ ra +++ + +d++   YG+ntGFG l++v+id+++ ++Lq nl+
  lcl|FitnessBrowser__Cola:Echvi_0202  17 PVTLERIYRVVSEGKRLELSSAAIERIQQCRAYLDDKIYKDEAAlyYGINTGFGYLQQVRIDRNEIQQLQYNLL 90 
                                          5899******************************9877666653358*************************** PP

                            TIGR01225  79 rsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLahlal 152
                                          +sHa+GvGe++++e+vR++l+++++sl++G+sgv+ e+++ lv++ n++vlPvv ++Gs+GasGDL PL+hl+l
  lcl|FitnessBrowser__Cola:Echvi_0202  91 QSHACGVGEKVPKELVRLMLLTKIESLSRGHSGVQLETVQRLVDFYNHDVLPVVYNQGSLGASGDLSPLSHLSL 164
                                          ************************************************************************** PP

                            TIGR01225 153 vliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalslea 226
                                           liG Ge+ feg+v ++a++L++ g +Pvtl++kEGl LinGtq+m +++v    +ae+l + ad++aa+s+++
  lcl|FitnessBrowser__Cola:Echvi_0202 165 PLIGMGEVYFEGKVCPSAQVLEQFGWQPVTLRSKEGLSLINGTQFMLSYGVHITQRAEALFRWADLIAAISVDG 238
                                          ************************************************************************** PP

                            TIGR01225 227 llgtskafdpdihevrphrgqiavaarlrellagseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevl 300
                                            g  ++f++ ih +r+h+gq+++aa+lr++l+gseia+s+  e++vqD+Ys RciPqvhGa +dtl++vk + 
  lcl|FitnessBrowser__Cola:Echvi_0202 239 FNGNLQPFNALIHRIRAHEGQVDTAASLRHYLEGSEIAQSK--EKQVQDPYSFRCIPQVHGASKDTLAFVKGTF 310
                                          ****************************************9..99***************************** PP

                            TIGR01225 301 aiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGl 374
                                          ++E++s+tDnP +f+de+e+ sgGnFHg+p+Ala d+laia+ae+g+iseRR+ +ll  +  +Lp FL++d+Gl
  lcl|FitnessBrowser__Cola:Echvi_0202 311 EREADSVTDNPNIFPDEDEILSGGNFHGQPLALAFDYLAIAMAEIGSISERRTYQLLSGQ-RGLPLFLVDDPGL 383
                                          *********************************************************875.59*********** PP

                            TIGR01225 375 nsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglef 448
                                          +sGlmi+qytaA++vsenk+L+ PasvDsi +s  qEDHvsmga +a k l+v +n+++++aiEll+aaq+lef
  lcl|FitnessBrowser__Cola:Echvi_0202 384 HSGLMIPQYTAASVVSENKQLCTPASVDSIVSSNGQEDHVSMGANGATKCLRVLDNLEKILAIELLTAAQALEF 457
                                          ************************************************************************** PP

                            TIGR01225 449 rkaektaaelekvyeavRevveeleeDRvlapDleavkellekesle 495
                                          r++ +++  +e+++   R+ v+  ++DRvl+ D+++  ++l+++s+e
  lcl|FitnessBrowser__Cola:Echvi_0202 458 RRPARSSEIVERLIGVYRDHVSFNAQDRVLSVDIKNTIKFLRDRSVE 504
                                          *****************************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (508 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.83
//
[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