Alignments for a candidate for hutH in Flavobacterium sp. LM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Flavobacterium sp. LM5

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate WP_078213149.1 BXU11_RS15100 histidine ammonia-lyase

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



>NCBI__GCF_002017945.1:WP_078213149.1
          Length = 504

 Score =  418 bits (1074), Expect = e-121
 Identities = 235/485 (48%), Positives = 320/485 (65%), Gaps = 6/485 (1%)

Query: 10  LTLETVNGIANGSIQAELCQQAIDKINASRHNVDV-MAASDKAIYGINTGFGPLCDTQIS 68
           LT E +  I        L ++A   I   R  +D  MA  ++ IYGINTGFG LC+ +IS
Sbjct: 12  LTFEALQEIVVFQKTIALSEEAKVNIQKCRDFLDKKMATHNEPIYGINTGFGSLCNVKIS 71

Query: 69  PAETHLLQKNLLITHAVGVGEPIAKSISKLMLITKVHALSQGFSGIRLDVVERMLAFIAL 128
                 LQ+NL+ +HA G GE +  +I +LML+ K+ +LS G SG++L  VER++ F   
Sbjct: 72  NENLTKLQENLVKSHACGTGEEVPFAIVQLMLLLKIQSLSYGHSGVQLQTVERLVDFYNN 131

Query: 129 DLIPVVPEQGSVGASGDLAPLSHLFLPLLGEGE-FWQGDKIVPAREALKAHGLEPLELHA 187
            + PVV   GS+GASGDLAPL+HL LPLLGEGE +++G+K V A+E L +   EP+ L +
Sbjct: 132 GIYPVVYTLGSLGASGDLAPLAHLSLPLLGEGEVYFEGNK-VAAKEILASFNWEPIILQS 190

Query: 188 KEGLALINGTQFILSHAITALTKMGYLLDLADLAGAMSIEGMQGSQSPFRAELHEIRPFA 247
           KEGLAL+NGTQF+ ++    + K   L   ADL GA+S+EG  G   PF   +H IRP  
Sbjct: 191 KEGLALLNGTQFMAAYGAHIIIKGHKLSYFADLIGAISLEGFDGRIEPFTELIHFIRPHK 250

Query: 248 GNIEVAARMRSFFKDSENMASHEDCDRVQDPYSLRCIPQVHGASRNAYNHLKELAEIEMN 307
           G I+ A RM  F + S+ +A  +    VQDPYS RCIPQVHGAS++A  ++K++ + E+N
Sbjct: 251 GQIQTAQRMNDFLEGSQIVAQPK--AHVQDPYSFRCIPQVHGASKDAMEYVKKVFKTEIN 308

Query: 308 SVTDNP-IVISAEEAISGGGFHGQPLAMVLDYTSIAAAELGNISDRRCYLLLEGLHGLPR 366
           SVTDNP I I +++ ISGG FHGQPLA+ LD+ +IA AELG+IS+RR Y L+ GL  LP 
Sbjct: 309 SVTDNPNIFIESDQIISGGNFHGQPLALALDFMAIALAELGSISERRTYQLISGLRNLPA 368

Query: 367 LLTTSGGLNSGMMIPQYVTAALVTENKSLCFPPSADSVPTSMGQEDHVSMGSISGRKLNQ 426
            L  + GLNSG MIPQY  A++V++NK L  P S DS+ +S GQEDHVSMG+    K  +
Sbjct: 369 FLVDNPGLNSGFMIPQYTAASIVSQNKQLATPSSVDSIVSSNGQEDHVSMGANGATKCLR 428

Query: 427 ILGNLEKIFAIELMYAAQAIDFRRPNRCSDIIEQNHALIREKVAKLEEDRLLKPDIDAII 486
           +L NLE+I AIELM A+QAI+FRRP + S+ IE      R++V  + EDR+L  DI+  I
Sbjct: 429 VLDNLERILAIELMNASQAIEFRRPLQSSNFIEMFLNSYRQEVPFVNEDRILHYDIEKTI 488

Query: 487 ALVKA 491
           + + +
Sbjct: 489 SFLNS 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: 569
Number of extensions: 20
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: 504
Length adjustment: 34
Effective length of query: 463
Effective length of database: 470
Effective search space:   217610
Effective search space used:   217610
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_078213149.1 BXU11_RS15100 (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.2169740.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-186  606.8   0.0   1.7e-186  606.5   0.0    1.0  1  NCBI__GCF_002017945.1:WP_078213149.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002017945.1:WP_078213149.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  606.5   0.0  1.7e-186  1.7e-186       3     491 ..       7     493 ..       5     501 .. 0.98

  Alignments for each domain:
  == domain 1  score: 606.5 bits;  conditional E-value: 1.7e-186
                             TIGR01225   3 ldgesltledleavarekarvelsaaaeeavaksraviee.ivaedktvYGvntGFGklasvkidkedlaeLq 74 
                                           + +e lt e+l+++++ ++ ++ls++a+ +++k r  +++ ++++++++YG+ntGFG+l +vki +e+l++Lq
  NCBI__GCF_002017945.1:WP_078213149.1   7 ISTELLTFEALQEIVVFQKTIALSEEAKVNIQKCRDFLDKkMATHNEPIYGINTGFGSLCNVKISNENLTKLQ 79 
                                           677889*******************************985378899*************************** PP

                             TIGR01225  75 rnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPL 147
                                           +nlv+sHa+G Ge+++ ++v ++l+l+++sl+ G+sgv+ +++e lv++ n++++Pvv + Gs+GasGDLAPL
  NCBI__GCF_002017945.1:WP_078213149.1  80 ENLVKSHACGTGEEVPFAIVQLMLLLKIQSLSYGHSGVQLQTVERLVDFYNNGIYPVVYTLGSLGASGDLAPL 152
                                           ************************************************************************* PP

                             TIGR01225 148 ahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaa 220
                                           ahl+l l+GeGe+ feg+ + a+e+La  + eP+ l++kEGlAL+nGtq+m+a+++  +++ +kl + ad+++
  NCBI__GCF_002017945.1:WP_078213149.1 153 AHLSLPLLGEGEVYFEGNKVAAKEILASFNWEPIILQSKEGLALLNGTQFMAAYGAHIIIKGHKLSYFADLIG 225
                                           ************************************************************************* PP

                             TIGR01225 221 alsleallgtskafdpdihevrphrgqiavaarlrellagseiaeshkdedrvqDaYslRciPqvhGavldtl 293
                                           a+sle+  g  ++f++ ih +rph+gqi++a+r+ ++l+gs+i+ +   + +vqD+Ys RciPqvhGa +d++
  NCBI__GCF_002017945.1:WP_078213149.1 226 AISLEGFDGRIEPFTELIHFIRPHKGQIQTAQRMNDFLEGSQIVAQP--KAHVQDPYSFRCIPQVHGASKDAM 296
                                           ********************************************988..899********************* PP

                             TIGR01225 294 dqvkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLpp 366
                                           ++vk+v ++E+ns+tDnP +f ++++++sgGnFHg+p+Alaldf+aia+aelg+iseRR+ +l+   l +Lp+
  NCBI__GCF_002017945.1:WP_078213149.1 297 EYVKKVFKTEINSVTDNPNIFIESDQIISGGNFHGQPLALALDFMAIALAELGSISERRTYQLIS-GLRNLPA 368
                                           ****************************************************************7.5789*** PP

                             TIGR01225 367 FLaedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEl 439
                                           FL++++GlnsG+mi+qytaA++vs+nk+La P+svDsi +s  qEDHvsmga +a k l+v +n++r++aiEl
  NCBI__GCF_002017945.1:WP_078213149.1 369 FLVDNPGLNSGFMIPQYTAASIVSQNKQLATPSSVDSIVSSNGQEDHVSMGANGATKCLRVLDNLERILAIEL 441
                                           ************************************************************************* PP

                             TIGR01225 440 laaaqglefrkaektaaelekvyeavRevveeleeDRvlapDleavkellek 491
                                           + a+q++efr++ +++  +e   +  R++v+ ++eDR+l +D+e+  ++l++
  NCBI__GCF_002017945.1:WP_078213149.1 442 MNASQAIEFRRPLQSSNFIEMFLNSYRQEVPFVNEDRILHYDIEKTISFLNS 493
                                           *********************************************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (504 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 34.87
//
[ok]

This GapMind analysis is from Sep 24 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 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