Alignments for a candidate for hutH in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Flavobacterium beibuense F44-8

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate WP_035134897.1 Q763_RS12750 histidine ammonia-lyase

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



>NCBI__GCF_000769915.1:WP_035134897.1
          Length = 502

 Score =  431 bits (1109), Expect = e-125
 Identities = 236/482 (48%), Positives = 320/482 (66%), Gaps = 4/482 (0%)

Query: 10  LTLETVNGIANGSIQAELCQQAIDKINASRHNVDV-MAASDKAIYGINTGFGPLCDTQIS 68
           L++E VN I     + EL ++A   I   R  +D  M +    IYGINTGFG L + +IS
Sbjct: 12  LSIEVVNEIITQGKKLELSEEARLNIEKCRTYLDEKMKSHSDPIYGINTGFGSLYNVKIS 71

Query: 69  PAETHLLQKNLLITHAVGVGEPIAKSISKLMLITKVHALSQGFSGIRLDVVERMLAFIAL 128
                 LQ+NL+ +HA G GE + + I K+ML+ K+ +LS G SG++L+ V+R++ F   
Sbjct: 72  NENLSKLQENLVKSHACGTGEEVPQEIVKIMLLLKIQSLSYGHSGVQLETVQRLIDFYNN 131

Query: 129 DLIPVVPEQGSVGASGDLAPLSHLFLPLLGEGEFWQGDKIVPAREALKAHGLEPLELHAK 188
           D++PVV  QGS+GASGDLAPL+HL LPLLGEGE        PA + L+  G +P+ L +K
Sbjct: 132 DILPVVYNQGSLGASGDLAPLAHLSLPLLGEGEVNMDGFRQPASKVLEKIGWKPIVLKSK 191

Query: 189 EGLALINGTQFILSHAITALTKMGYLLDLADLAGAMSIEGMQGSQSPFRAELHEIRPFAG 248
           EGLAL+NGTQF+ S+ +  L K      LAD+ GA+S+EG  G   PF   +H +RP  G
Sbjct: 192 EGLALLNGTQFMSSYGVYVLLKSIKYSYLADVIGAISLEGFDGRIEPFNELIHMVRPHKG 251

Query: 249 NIEVAARMRSFFKDSENMASHEDCDRVQDPYSLRCIPQVHGASRNAYNHLKELAEIEMNS 308
            I  A R     +DSE +A  +    VQDPYS RCIPQVHGA+++  +++K++   E+NS
Sbjct: 252 QIVTAQRFNQLLEDSEIIAHPK--QHVQDPYSFRCIPQVHGATKDTIDYVKKVFRTEINS 309

Query: 309 VTDNP-IVISAEEAISGGGFHGQPLAMVLDYTSIAAAELGNISDRRCYLLLEGLHGLPRL 367
           VTDNP I I +++ ISGG FHGQPLA+ LD+  IA +ELG+IS+RR Y L+ GL GLP  
Sbjct: 310 VTDNPNIFIDSDQIISGGNFHGQPLALTLDFLGIALSELGSISERRTYQLISGLRGLPPF 369

Query: 368 LTTSGGLNSGMMIPQYVTAALVTENKSLCFPPSADSVPTSMGQEDHVSMGSISGRKLNQI 427
           L  + GLNSG MIPQY  A++V++NK LC P SADS+ +S GQEDHVSMG+ +  K  +I
Sbjct: 370 LVANPGLNSGFMIPQYTAASIVSQNKQLCTPASADSIVSSNGQEDHVSMGANAATKALRI 429

Query: 428 LGNLEKIFAIELMYAAQAIDFRRPNRCSDIIEQNHALIREKVAKLEEDRLLKPDIDAIIA 487
           + NLE+I AIELM A+QAI+FRRP + SD IE      RE+V  +E+DR+L  DI+  IA
Sbjct: 430 IENLERILAIELMNASQAIEFRRPLKSSDFIEMFLKSYREEVPLVEDDRILHYDIENTIA 489

Query: 488 LV 489
            +
Sbjct: 490 FL 491


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: 19
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: 502
Length adjustment: 34
Effective length of query: 463
Effective length of database: 468
Effective search space:   216684
Effective search space used:   216684
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 WP_035134897.1 Q763_RS12750 (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.3176102.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-190  618.4   0.0   5.4e-190  618.0   0.0    1.0  1  NCBI__GCF_000769915.1:WP_035134897.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000769915.1:WP_035134897.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.0   0.0  5.4e-190  5.4e-190       5     494 ..       9     496 ..       6     501 .. 0.97

  Alignments for each domain:
  == domain 1  score: 618.0 bits;  conditional E-value: 5.4e-190
                             TIGR01225   5 gesltledleavarekarvelsaaaeeavaksravieeiva.edktvYGvntGFGklasvkidkedlaeLqrn 76 
                                           +e l++e ++++ ++++++els++a+ +++k r+ ++e ++ +  ++YG+ntGFG+l +vki +e+l +Lq+n
  NCBI__GCF_000769915.1:WP_035134897.1   9 SELLSIEVVNEIITQGKKLELSEEARLNIEKCRTYLDEKMKsHSDPIYGINTGFGSLYNVKISNENLSKLQEN 81 
                                           66788999****************************876661578**************************** PP

                             TIGR01225  77 lvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLah 149
                                           lv+sHa+G Ge++++e+v+++l+l+++sl+ G+sgv+ e+++ l+++ n+++lPvv ++Gs+GasGDLAPLah
  NCBI__GCF_000769915.1:WP_035134897.1  82 LVKSHACGTGEEVPQEIVKIMLLLKIQSLSYGHSGVQLETVQRLIDFYNNDILPVVYNQGSLGASGDLAPLAH 154
                                           ************************************************************************* PP

                             TIGR01225 150 lalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaal 222
                                           l+l l+GeGe++++g +++a+++L++ g +P+ lk+kEGlAL+nGtq+m++++v  l +  k  + ad+++a+
  NCBI__GCF_000769915.1:WP_035134897.1 155 LSLPLLGEGEVNMDGFRQPASKVLEKIGWKPIVLKSKEGLALLNGTQFMSSYGVYVLLKSIKYSYLADVIGAI 227
                                           ************************************************************************* PP

                             TIGR01225 223 sleallgtskafdpdihevrphrgqiavaarlrellagseiaeshkdedrvqDaYslRciPqvhGavldtldq 295
                                           sle+  g  ++f++ ih vrph+gqi++a+r+ +ll++sei  +   +++vqD+Ys RciPqvhGa++dt+d+
  NCBI__GCF_000769915.1:WP_035134897.1 228 SLEGFDGRIEPFNELIHMVRPHKGQIVTAQRFNQLLEDSEIIAHP--KQHVQDPYSFRCIPQVHGATKDTIDY 298
                                           ******************************************998..899*********************** PP

                             TIGR01225 296 vkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFL 368
                                           vk+v  +E+ns+tDnP +f d+++++sgGnFHg+p+Al+ldfl ia++elg+iseRR+ +l+   l +LppFL
  NCBI__GCF_000769915.1:WP_035134897.1 299 VKKVFRTEINSVTDNPNIFIDSDQIISGGNFHGQPLALTLDFLGIALSELGSISERRTYQLIS-GLRGLPPFL 370
                                           *************************************************************97.588****** PP

                             TIGR01225 369 aedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiElla 441
                                           ++++GlnsG+mi+qytaA++vs+nk+L+ Pas+Dsi +s  qEDHvsmga aa k+l+++en++r++aiEl+ 
  NCBI__GCF_000769915.1:WP_035134897.1 371 VANPGLNSGFMIPQYTAASIVSQNKQLCTPASADSIVSSNGQEDHVSMGANAATKALRIIENLERILAIELMN 443
                                           ************************************************************************* PP

                             TIGR01225 442 aaqglefrkaektaaelekvyeavRevveeleeDRvlapDleavkellekesl 494
                                           a+q++efr++ k++  +e   +  Re+v+ +e+DR+l +D+e+   +l++ ++
  NCBI__GCF_000769915.1:WP_035134897.1 444 ASQAIEFRRPLKSSDFIEMFLKSYREEVPLVEDDRILHYDIENTIAFLNNMQI 496
                                           ******************************************99999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (502 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 17.35
//
[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)
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Protein sequences (fasta format)
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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 2024 update 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