Alignments for a candidate for PS417_11890 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Herbaspirillum seropedicae SmR1

Align Inositol transport system ATP-binding protein (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein

Query= reanno::WCS417:GFF2332
         (517 letters)



>FitnessBrowser__HerbieS:HSERO_RS05250
          Length = 520

 Score =  469 bits (1206), Expect = e-136
 Identities = 251/492 (51%), Positives = 340/492 (69%), Gaps = 4/492 (0%)

Query: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82
           ++ + N+ K FPGV+AL + Q  +  G V ALMGENGAGKSTLMKI++G+YQ D+G+I L
Sbjct: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81

Query: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHM-VNHREMHRCT 141
            GKP+    P  AQ  GI +IHQELNLM H+S A+NI+IGRE   ++ + ++  E++R  
Sbjct: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141

Query: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201
           A + AR+R+++DP   VG L++A +QMVEIAKA+S+DS +LIMDEPT+A+   E+A LF 
Sbjct: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201

Query: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261
           II DL++QG GIVYI+HKM+E+  IAD V+V RDG YI        + D++ISMMVGR L
Sbjct: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261

Query: 262 S--QLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319
              Q  P  +T   D++L VR L      +DVSF L  GEILG AGLMG+GRT VA  IF
Sbjct: 262 DGEQRIP-PDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIF 320

Query: 320 GITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379
           G  P  +G+I + G    I  P  A+  G   L+EDRK  GL   + V  N+ ++ +  +
Sbjct: 321 GADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRF 380

Query: 380 TGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILD 439
           T  GF+ Q+A+R   +   ++L +KTPS+EQ    LSGGNQQK ++A+WL+ +  +L  D
Sbjct: 381 TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFD 440

Query: 440 EPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRS 499
           EPTRGIDVGAK+EIY+L+  LA +G A++MISSELPEVL MS RV+VM EG + G L R+
Sbjct: 441 EPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARA 500

Query: 500 EATQEKVMQLAS 511
           +ATQEK+MQLA+
Sbjct: 501 DATQEKIMQLAT 512



 Score =  100 bits (250), Expect = 1e-25
 Identities = 62/221 (28%), Positives = 117/221 (52%), Gaps = 6/221 (2%)

Query: 293 FDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALL 352
           F+L AGE+  + G  G+G++ + + + G+    SG I LDGK V I++P  A   G  ++
Sbjct: 43  FELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII 102

Query: 353 TEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKT-PSLEQC 411
            ++  L      LS  +N+ +   P      FI +  L      +  ++R+   PS    
Sbjct: 103 HQELNLMNH---LSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMDPSTP-- 157

Query: 412 IDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMIS 471
           +  L+   QQ   +A+ L  + R+LI+DEPT  ++    AE++R+I  L ++G+ ++ IS
Sbjct: 158 VGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYIS 217

Query: 472 SELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512
            ++ E+  ++DRV VM +G+ + T+   E + + ++ +  G
Sbjct: 218 HKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258



 Score = 89.0 bits (219), Expect = 4e-22
 Identities = 70/254 (27%), Positives = 119/254 (46%), Gaps = 11/254 (4%)

Query: 13  LQPQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGI 72
           + P T     +LE+  +++G     A+ DV   +R G +L   G  GAG++ + + I G 
Sbjct: 267 IPPDTSRNDVVLEVRGLNRGR----AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGA 322

Query: 73  YQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQE---LNLMPHMSIAENIWIGRE-QLNS 128
              +AGEI + G   V ++P  A   GI  + ++     L   M +  NI +    +   
Sbjct: 323 DPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTR 382

Query: 129 LHMVNHREMHRCTAELLARLRINLDP-EEQVGNLSIAERQMVEIAKAVSYDSDILIMDEP 187
           +  ++ R +       + +L I     E+Q   LS   +Q + IAK +  D DIL  DEP
Sbjct: 383 VGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEP 442

Query: 188 TSAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADS 246
           T  I     + ++ ++  L  QGK IV I+ ++ EV  ++  V V  +G   G L RAD+
Sbjct: 443 TRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADA 502

Query: 247 MNSDSLISMMVGRE 260
              + ++ +   RE
Sbjct: 503 -TQEKIMQLATQRE 515


Lambda     K      H
   0.320    0.136    0.381 

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: 592
Number of extensions: 31
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 517
Length of database: 520
Length adjustment: 35
Effective length of query: 482
Effective length of database: 485
Effective search space:   233770
Effective search space used:   233770
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)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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

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