Alignments for a candidate for glcB in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Herbaspirillum seropedicae SmR1

Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate HSERO_RS15200 HSERO_RS15200 malate synthase

Query= reanno::BFirm:BPHYT_RS12305
         (536 letters)



>FitnessBrowser__HerbieS:HSERO_RS15200
          Length = 528

 Score =  848 bits (2190), Expect = 0.0
 Identities = 414/528 (78%), Positives = 462/528 (87%), Gaps = 1/528 (0%)

Query: 9   SSLQLPQGMEITAEIKPGYDAILSREALELVAALHRTFEPRRQQLLQARAERTKRLDAGE 68
           + L+LP GMEI+ +IKPGY+ IL+ EAL LVA L R FE RRQ+LL ARAER KRLDAGE
Sbjct: 2   TQLKLPTGMEISGDIKPGYENILTFEALSLVAKLSRAFEGRRQELLAARAERVKRLDAGE 61

Query: 69  RPDFLAETKSVRDGDWTIAPLPQDLQCRRVEITGPVERKMIINALNSGADSYMTDFEDSN 128
           RPDFL ET+S+R GDW IAP+P+ L+CRRVEITGPVERKM+INA NSGADSYMTDFEDSN
Sbjct: 62  RPDFLKETESIRTGDWKIAPIPEALKCRRVEITGPVERKMVINAFNSGADSYMTDFEDSN 121

Query: 129 APSWDNQITGHINLKDAVRRTISLEQNGKSYTLNDKVATLIVRPRGWHLDEKHVKVDGKR 188
           +P WDNQI+G INL DA+RRTISLE NGKSY LNDK+ATL+VRPRGWHLDEKHV +DGKR
Sbjct: 122 SPVWDNQISGQINLYDAIRRTISLESNGKSYKLNDKIATLVVRPRGWHLDEKHVTLDGKR 181

Query: 189 VSGGIFDFALFMVHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEAVGVPRGTI 248
           +SGGIFDFALF+ HNAKE +ARG+GPYFYLPKMESHLEARLWNDIFV AQ  +G+P+GTI
Sbjct: 182 ISGGIFDFALFLFHNAKEQLARGAGPYFYLPKMESHLEARLWNDIFVMAQNEIGLPQGTI 241

Query: 249 RATVLIETIVAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKADRDFCLADRSQITM 308
           +ATVLIETI AAFEM+EILYELREHS+GLNAGRWDYIFS IKKFK D+DFCLADR+++TM
Sbjct: 242 KATVLIETITAAFEMEEILYELREHSAGLNAGRWDYIFSCIKKFKNDKDFCLADRAKVTM 301

Query: 309 TSPFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMSGVRSDKARDAGDGYD 368
           TSPFMRAYALLLLKTCH+R APAIGGMSALIPIKNDP  N  AM G+ +DK RDA DGYD
Sbjct: 302 TSPFMRAYALLLLKTCHKRGAPAIGGMSALIPIKNDPEKNAIAMQGIINDKRRDATDGYD 361

Query: 369 GGWVAHPGLVPIAMEEFVKVLGDKPNQIGKQRDDVLVTATDLTDFRPEAPITEGGLRNNI 428
           GGWVAHPGLV  +M+EFV VLGDKPNQ  KQR DV V A DL +F+PE PITE GLR NI
Sbjct: 362 GGWVAHPGLVEASMKEFVAVLGDKPNQFEKQRPDVDVKAADLLNFQPETPITEAGLRYNI 421

Query: 429 NVGIHYLGAWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRKVTAELVRE 488
           NVGIHYLGAWLAGNGCVPIHNLMEDAATAEISR+QVWQWIRS KG LEDGRKVTA++VR 
Sbjct: 422 NVGIHYLGAWLAGNGCVPIHNLMEDAATAEISRAQVWQWIRSAKGNLEDGRKVTADMVRA 481

Query: 489 LSAQELEKVKQAVGGDTKPYERAAQIFEEMSTSEQFTDFLTLPLYEEI 536
           +  +EL KVKQ V GD   Y+RAA+IFEEMSTSE F +FLTLPLYEEI
Sbjct: 482 MIPEELAKVKQ-VAGDGPTYDRAAKIFEEMSTSETFAEFLTLPLYEEI 528


Lambda     K      H
   0.318    0.134    0.397 

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: 819
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: 536
Length of database: 528
Length adjustment: 35
Effective length of query: 501
Effective length of database: 493
Effective search space:   246993
Effective search space used:   246993
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 HSERO_RS15200 HSERO_RS15200 (malate synthase)
to HMM TIGR01344 (aceB: malate synthase A (EC 2.3.3.9))

# 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.carbon/TIGR01344.hmm
# target sequence database:        /tmp/gapView.6165.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01344  [M=511]
Accession:   TIGR01344
Description: malate_syn_A: malate synthase A
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.1e-233  760.1   0.0   4.6e-233  760.0   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS15200  HSERO_RS15200 malate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS15200  HSERO_RS15200 malate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  760.0   0.0  4.6e-233  4.6e-233       1     510 [.      23     528 .]      23     528 .] 0.98

  Alignments for each domain:
  == domain 1  score: 760.0 bits;  conditional E-value: 4.6e-233
                                  TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrr 68 
                                                +lt eal+++a+l+r f+ rr+ella+r+++  +ld+ge++dfl+et++ir +dwk+a+ip++l+ rr
  lcl|FitnessBrowser__HerbieS:HSERO_RS15200  23 ILTFEALSLVAKLSRAFEGRRQELLAARAERVKRLDAGERPDFLKETESIRTGDWKIAPIPEALKCRR 90 
                                                79****************************************************************** PP

                                  TIGR01344  69 veitGPvdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalka 136
                                                veitGPv+rkmvina+n++a  +++dfeds+sP w+n ++Gqinl+dair++i+    ++gk+y+l+ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS15200  91 VEITGPVERKMVINAFNSGADSYMTDFEDSNSPVWDNQISGQINLYDAIRRTISLE--SNGKSYKLND 156
                                                ******************************************************98..7********* PP

                                  TIGR01344 137 klavlivrprGwhlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwn 204
                                                k a+l+vrprGwhl e+h+++dgk isg ++df+l++fhna+e+l++G GPyfylPk+eshlearlwn
  lcl|FitnessBrowser__HerbieS:HSERO_RS15200 157 KIATLVVRPRGWHLDEKHVTLDGKRISGGIFDFALFLFHNAKEQLARGAGPYFYLPKMESHLEARLWN 224
                                                ******************************************************************** PP

                                  TIGR01344 205 dvfllaqevlglprGtikatvlietlpaafemdeilyelrehssGlncGrwdyifslikklkkaeevv 272
                                                d+f++aq+++glp+Gtikatvliet++aafem+eilyelrehs+Gln+Grwdyifs+ikk+k+++++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS15200 225 DIFVMAQNEIGLPQGTIKATVLIETITAAFEMEEILYELREHSAGLNAGRWDYIFSCIKKFKNDKDFC 292
                                                ******************************************************************** PP

                                  TIGR01344 273 lPdrdavtmdkaflnaysklliqtchrrgafalGGmaafiPikddpaaneaalekvradkereaknGh 340
                                                l dr +vtm+++f++ay+ ll++tch+rga a+GGm+a iPik+dp+ n  a++ + +dk r+a++G+
  lcl|FitnessBrowser__HerbieS:HSERO_RS15200 293 LADRAKVTMTSPFMRAYALLLLKTCHKRGAPAIGGMSALIPIKNDPEKNAIAMQGIINDKRRDATDGY 360
                                                ******************************************************************** PP

                                  TIGR01344 341 dGtwvahPdlvevalevfdevlge.pnqldrvrledvsitaaellev.kdasrteeGlrenirvglry 406
                                                dG wvahP+lve +++ f +vlg+ pnq +++r  dv + aa+ll+  +++  te+Glr ni+vg++y
  lcl|FitnessBrowser__HerbieS:HSERO_RS15200 361 DGGWVAHPGLVEASMKEFVAVLGDkPNQFEKQR-PDVDVKAADLLNFqPETPITEAGLRYNINVGIHY 427
                                                ***********************999****988.9***********9789999*************** PP

                                  TIGR01344 407 ieawlrGsGavpiynlmedaataeisraqlwqwikhGv.vledGekvtselvrdllkeeleklkkesg 473
                                                + awl G+G+vpi+nlmedaataeisraq+wqwi+  +  ledG+kvt+++vr ++ eel+k+k+ +g
  lcl|FitnessBrowser__HerbieS:HSERO_RS15200 428 LGAWLAGNGCVPIHNLMEDAATAEISRAQVWQWIRSAKgNLEDGRKVTADMVRAMIPEELAKVKQVAG 495
                                                **********************************988647************************9977 PP

                                  TIGR01344 474 keeyakarleeaaellerlvlseeledfltlpaydel 510
                                                ++    + +++aa+++e++++se++++fltlp+y+e+
  lcl|FitnessBrowser__HerbieS:HSERO_RS15200 496 DG----PTYDRAAKIFEEMSTSETFAEFLTLPLYEEI 528
                                                66....59**************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (528 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.00
//
[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)
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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 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