Alignments for a candidate for hisC in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Herbaspirillum seropedicae SmR1

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate HSERO_RS23520 HSERO_RS23520 histidinol-phosphate aminotransferase

Query= reanno::psRCH2:GFF3234
         (348 letters)



>FitnessBrowser__HerbieS:HSERO_RS23520
          Length = 360

 Score =  474 bits (1221), Expect = e-138
 Identities = 238/353 (67%), Positives = 275/353 (77%), Gaps = 6/353 (1%)

Query: 1   MSKFWSPFVKDLVPYVPGEQPKLSKLVKLNTNENPYGPSPRAIAAMQAELNDSLRLYPDP 60
           MSKFWSP V  L PY PGEQPK+++LVKLNTNE+PYGPSP A+ A+  E++DSLRLYP+P
Sbjct: 1   MSKFWSPIVSRLTPYTPGEQPKIARLVKLNTNESPYGPSPLALQAIAREVSDSLRLYPNP 60

Query: 61  NGERLKQAVADYY---GVQPAQVFVGNGSDEVLAHAFHGLFQHAGPLLFPDISYSFYPVY 117
           + E LKQA+A  +   GV   +VFVGNGSDEVLAHAFH L QH  P+LFPDI+YSFYP Y
Sbjct: 61  DAEPLKQAIARRHAADGVSVREVFVGNGSDEVLAHAFHALLQHGKPILFPDITYSFYPTY 120

Query: 118 CGLYGIAYETVALDEQFQIDVADY---NRPNGGIIFPNPNAPTGCLLALEAIERLLQANT 174
            GLY + Y  V L E F +   DY    +  GGIIFPNPNAPTGCLL L  +ER+LQ N 
Sbjct: 121 AGLYQVEYRAVPLAEDFTLRSEDYLGHGQAIGGIIFPNPNAPTGCLLGLADVERILQGNP 180

Query: 175 ETVVLVDEAYVDFGGESAIALVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALER 234
           E VV+VDEAY+DFGG+SAI LV RYPNLLV QTLSKSR+LAG+RVG AVGH DLI+ALER
Sbjct: 181 ERVVVVDEAYIDFGGQSAIPLVQRYPNLLVVQTLSKSRALAGMRVGFAVGHADLIDALER 240

Query: 235 IKNSFNSYPLDRIAIAGAAAAFEDRAYFQQTCQQVIDSREAVVAAMQGLGFEVLPSAANF 294
           +KNSFNSYPLDR AIAGA AA ED  YF++TC  VI SR A+ A + GLGF+VLPSAANF
Sbjct: 241 VKNSFNSYPLDRPAIAGATAAIEDEDYFRKTCNMVIASRTALAAQLAGLGFQVLPSAANF 300

Query: 295 IFARHPQRDAATIAASLREQGVIVRHFKQRRIEQFLRITIGTPEQNQALLEAL 347
           +F RHPQ DAA +AA+LR  G+IVRHFK  RI QFLRITIGT E    L+EAL
Sbjct: 301 LFVRHPQHDAAQLAAALRADGIIVRHFKSERISQFLRITIGTDEDCGVLVEAL 353


Lambda     K      H
   0.320    0.137    0.401 

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: 485
Number of extensions: 22
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: 348
Length of database: 360
Length adjustment: 29
Effective length of query: 319
Effective length of database: 331
Effective search space:   105589
Effective search space used:   105589
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: 49 (23.5 bits)

Align candidate HSERO_RS23520 HSERO_RS23520 (histidinol-phosphate aminotransferase)
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))

# 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.aa/TIGR01141.hmm
# target sequence database:        /tmp/gapView.2206452.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01141  [M=349]
Accession:   TIGR01141
Description: hisC: histidinol-phosphate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
    2.7e-96  308.4   0.0      3e-96  308.3   0.0    1.0  1  FitnessBrowser__HerbieS:HSERO_RS23520  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS23520  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.3   0.0     3e-96     3e-96       4     348 ..       9     355 ..       6     356 .. 0.95

  Alignments for each domain:
  == domain 1  score: 308.3 bits;  conditional E-value: 3e-96
                              TIGR01141   4 ikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpqalelkealakylg...ve 71 
                                            ++ l+pY+pg++ +     vkLn+nE+P+gps+ +++a+ +e++ +l++Yp+p+a  lk+a+a++     v+
  FitnessBrowser__HerbieS:HSERO_RS23520   9 VSRLTPYTPGEQPKIA-RLVKLNTNESPYGPSPLALQAIAREVSdSLRLYPNPDAEPLKQAIARRHAadgVS 79 
                                            7899*****9766666.6*************************999*****************9988889** PP

                              TIGR01141  72 eenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakek 143
                                            + ++++gnGsde++   ++a+l+ g+ +l+++ tys Y+++a ++++e++ vpl+ed++   e+ l  + + 
  FitnessBrowser__HerbieS:HSERO_RS23520  80 VREVFVGNGSDEVLAHAFHALLQHGKPILFPDITYSFYPTYAGLYQVEYRAVPLAEDFTLRSEDYL-GHGQA 150
                                            *********************************************************999999999.88888 PP

                              TIGR01141 144 vklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLA 215
                                            +  + + +Pn+PtG ll  +++e++l+   + +VVvDeAYi+F ++ s+++l+++ypnl+v++TlSK+ +LA
  FitnessBrowser__HerbieS:HSERO_RS23520 151 IGGIIFPNPNAPTGCLLGLADVERILQGNPERVVVVDEAYIDFGGQ-SAIPLVQRYPNLLVVQTLSKSRALA 221
                                            999999**********************779**************7.************************* PP

                              TIGR01141 216 glRvGyaianaeiiealekvrapyn...vsslaleaavaalrdsdkiektveevkkererlleelkklegle 284
                                            g+RvG+a+++a++i+ale+v++++n   ++++a + a+aa++d+d+++kt + v+++r+ l ++l+ l g++
  FitnessBrowser__HerbieS:HSERO_RS23520 222 GMRVGFAVGHADLIDALERVKNSFNsypLDRPAIAGATAAIEDEDYFRKTCNMVIASRTALAAQLAGL-GFQ 292
                                            *********************87543339***************************************.8** PP

                              TIGR01141 285 vyeSkaNFvlikvke.daeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                            v +S aNF++++ ++ da++l+ al   giivR++ks    ++++lRit+Gt+e++  l+eal++
  FitnessBrowser__HerbieS:HSERO_RS23520 293 VLPSAANFLFVRHPQhDAAQLAAALRADGIIVRHFKSE--RISQFLRITIGTDEDCGVLVEALRR 355
                                            **************99********************88..48*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (360 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.10
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis