Aligments for a candidate for hutH in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments for a candidate for hutH in Klebsiella michiganensis M5al

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate BWI76_RS08740 BWI76_RS08740 histidine ammonia-lyase

Query= reanno::Koxy:BWI76_RS08740
         (507 letters)



>FitnessBrowser__Koxy:BWI76_RS08740
          Length = 507

 Score =  978 bits (2528), Expect = 0.0
 Identities = 507/507 (100%), Positives = 507/507 (100%)

Query: 1   MNALTLIPGQLSLSQLRDVYSQPLKLALDESAFAAIDDSVACVNAILAEGRTAYGINTGF 60
           MNALTLIPGQLSLSQLRDVYSQPLKLALDESAFAAIDDSVACVNAILAEGRTAYGINTGF
Sbjct: 1   MNALTLIPGQLSLSQLRDVYSQPLKLALDESAFAAIDDSVACVNAILAEGRTAYGINTGF 60

Query: 61  GLLAQTRISTEDLENLQRSLVLSHAAGVGEPLDDDLARLIMVLKINSLSRGFSGIRLSVI 120
           GLLAQTRISTEDLENLQRSLVLSHAAGVGEPLDDDLARLIMVLKINSLSRGFSGIRLSVI
Sbjct: 61  GLLAQTRISTEDLENLQRSLVLSHAAGVGEPLDDDLARLIMVLKINSLSRGFSGIRLSVI 120

Query: 121 QALIGLVNAGVTPWIPAKGSVGASGDLAPLAHMSLTLLGEGKARVRGGEWLPATEALRQA 180
           QALIGLVNAGVTPWIPAKGSVGASGDLAPLAHMSLTLLGEGKARVRGGEWLPATEALRQA
Sbjct: 121 QALIGLVNAGVTPWIPAKGSVGASGDLAPLAHMSLTLLGEGKARVRGGEWLPATEALRQA 180

Query: 181 GLEPITLAAKEGLALLNGTQASTAFALRGLFEAEDLFSSAVVCGALTTEAALGSRRPFDP 240
           GLEPITLAAKEGLALLNGTQASTAFALRGLFEAEDLFSSAVVCGALTTEAALGSRRPFDP
Sbjct: 181 GLEPITLAAKEGLALLNGTQASTAFALRGLFEAEDLFSSAVVCGALTTEAALGSRRPFDP 240

Query: 241 RIHEARGQRGQIDAAALYRHLLTDDSAISQSHHNCTKVQDPYSLRCQPQVMGACLTQLRQ 300
           RIHEARGQRGQIDAAALYRHLLTDDSAISQSHHNCTKVQDPYSLRCQPQVMGACLTQLRQ
Sbjct: 241 RIHEARGQRGQIDAAALYRHLLTDDSAISQSHHNCTKVQDPYSLRCQPQVMGACLTQLRQ 300

Query: 301 AAEVLLVEANAVSDNPLVFASENDVISGGNFHAEPVAMAADNIALAIAEIGSLSERRIAL 360
           AAEVLLVEANAVSDNPLVFASENDVISGGNFHAEPVAMAADNIALAIAEIGSLSERRIAL
Sbjct: 301 AAEVLLVEANAVSDNPLVFASENDVISGGNFHAEPVAMAADNIALAIAEIGSLSERRIAL 360

Query: 361 MMDSHMSQLPPFLVKNGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVS 420
           MMDSHMSQLPPFLVKNGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVS
Sbjct: 361 MMDSHMSQLPPFLVKNGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVS 420

Query: 421 MAPAAGRRLWAMAENTRGVLAVEWLASVQGLDMREGLTSSPLLEEARHLLRERVTHYTED 480
           MAPAAGRRLWAMAENTRGVLAVEWLASVQGLDMREGLTSSPLLEEARHLLRERVTHYTED
Sbjct: 421 MAPAAGRRLWAMAENTRGVLAVEWLASVQGLDMREGLTSSPLLEEARHLLRERVTHYTED 480

Query: 481 RFFAPDIENAIALLAARHLTRLLPAVL 507
           RFFAPDIENAIALLAARHLTRLLPAVL
Sbjct: 481 RFFAPDIENAIALLAARHLTRLLPAVL 507


Lambda     K      H
   0.318    0.132    0.374 

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: 872
Number of extensions: 16
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: 507
Length of database: 507
Length adjustment: 34
Effective length of query: 473
Effective length of database: 473
Effective search space:   223729
Effective search space used:   223729
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate BWI76_RS08740 BWI76_RS08740 (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.11220.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.6e-219  714.8   3.6   2.9e-219  714.6   3.6    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS08740  BWI76_RS08740 histidine ammonia-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS08740  BWI76_RS08740 histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.6   3.6  2.9e-219  2.9e-219       3     499 ..       6     504 ..       4     507 .] 0.98

  Alignments for each domain:
  == domain 1  score: 714.6 bits;  conditional E-value: 2.9e-219
                               TIGR01225   3 ldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeL 73 
                                             l +++l+l++l+ v+ +  +++l+++a +a++ s a++++i+ae +t YG+ntGFG la+++i +edl++L
  lcl|FitnessBrowser__Koxy:BWI76_RS08740   6 LIPGQLSLSQLRDVYSQPLKLALDESAFAAIDDSVACVNAILAEGRTAYGINTGFGLLAQTRISTEDLENL 76 
                                             667899***************************************************************** PP

                               TIGR01225  74 qrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDL 144
                                             qr+lv+sHaaGvGepl+++++R+++vl++nsl++G+sg+r  v+++l+ l+na+v+P +p kGsvGasGDL
  lcl|FitnessBrowser__Koxy:BWI76_RS08740  77 QRSLVLSHAAGVGEPLDDDLARLIMVLKINSLSRGFSGIRLSVIQALIGLVNAGVTPWIPAKGSVGASGDL 147
                                             *********************************************************************** PP

                               TIGR01225 145 APLahlalvliGeGeae.fegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaeklle 214
                                             APLah++l+l+GeG+a+   ge+++a+eaL++agleP+tl+akEGlAL+nGtq++ta+a+++l++ae+l +
  lcl|FitnessBrowser__Koxy:BWI76_RS08740 148 APLAHMSLTLLGEGKARvRGGEWLPATEALRQAGLEPITLAAKEGLALLNGTQASTAFALRGLFEAEDLFS 218
                                             *****************55689************************************************* PP

                               TIGR01225 215 sadiaaalsleallgtskafdpdihevrphrgqiavaarlrella.gseiaeshkdedrvqDaYslRciPq 284
                                             sa +++al++ea+lg++++fdp+ihe+r++rgqi+ aa  r+ll+ +s i++sh+++++vqD+YslRc+Pq
  lcl|FitnessBrowser__Koxy:BWI76_RS08740 219 SAVVCGALTTEAALGSRRPFDPRIHEARGQRGQIDAAALYRHLLTdDSAISQSHHNCTKVQDPYSLRCQPQ 289
                                             *******************************************9989************************ PP

                               TIGR01225 285 vhGavldtldqvkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRier 355
                                             v+Ga+l++l+q++evl +E+n+++DnPlvfa e++v+sgGnFH+epvA+a+d++a+aiae+g++seRRi++
  lcl|FitnessBrowser__Koxy:BWI76_RS08740 290 VMGACLTQLRQAAEVLLVEANAVSDNPLVFASENDVISGGNFHAEPVAMAADNIALAIAEIGSLSERRIAL 360
                                             *********************************************************************** PP

                               TIGR01225 356 lldpalseLppFLaedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarklle 426
                                             ++d ++s+LppFL++++G+nsG+miaq+taAaL+senkaL+hP+svDs+ptsanqEDHvsm+ aa+r+l+ 
  lcl|FitnessBrowser__Koxy:BWI76_RS08740 361 MMDSHMSQLPPFLVKNGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSMAPAAGRRLWA 431
                                             *********************************************************************** PP

                               TIGR01225 427 vvenvrrviaiEllaaaqglefrkaektaaelekvyeavRevveeleeDRvlapDleavkellekesleaa 497
                                             ++en+r v+a+E+la++qgl++r+  ++++ le++++++Re v++++eDR++apD+e++  ll++++l+  
  lcl|FitnessBrowser__Koxy:BWI76_RS08740 432 MAENTRGVLAVEWLASVQGLDMREGLTSSPLLEEARHLLRERVTHYTEDRFFAPDIENAIALLAARHLTRL 502
                                             ****************************************************************9999877 PP

                               TIGR01225 498 ve 499
                                             ++
  lcl|FitnessBrowser__Koxy:BWI76_RS08740 503 LP 504
                                             65 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (507 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: 9.74
//
[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)
Organisms (tab-delimited)
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, or view the source code.

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