Alignments for a candidate for BPHYT_RS34245 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS34245 in Herbaspirillum seropedicae SmR1

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate HSERO_RS05175 HSERO_RS05175 sugar ABC transporter ATP-binding protein

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__HerbieS:HSERO_RS05175
          Length = 516

 Score =  298 bits (764), Expect = 2e-85
 Identities = 184/517 (35%), Positives = 278/517 (53%), Gaps = 28/517 (5%)

Query: 5   MSELTSSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLR 64
           MS  T + P++E   + K F    AL DV +R+ PGE H L+G+NGAGKSTL+ +LTG+ 
Sbjct: 3   MSVGTQARPMLELSGIHKAFAGVKALTDVGLRLFPGEVHTLMGQNGAGKSTLIKVLTGVH 62

Query: 65  KPDTGEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDW 124
           +PD G++   G A    +  +A    ++ VYQ   +  +LSVAEN+F+ R P R G IDW
Sbjct: 63  EPDGGKIELDGRAIAPASTLEAQALGISTVYQEVNLCPNLSVAENIFVGRYPTRFGRIDW 122

Query: 125 QAMRRDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGD 184
           +++   +R LL   +ID+   A      +  +Q+V I+RALS  A+ +ILDEPT+ LD  
Sbjct: 123 KSVHTQSRQLLQQLQIDIDVAAPLSSYPLAIQQMVAISRALSVSAKVLILDEPTSSLDEA 182

Query: 185 EIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIE 244
           E+++LF+ +  L+ +G+  LF++H L + YEI   +TVLR+        VS L R  L+ 
Sbjct: 183 EVQQLFKVLRRLREQGMAILFVTHFLDQTYEISDRITVLRNGVREGEYLVSELSRLDLVN 242

Query: 245 AMTG---------ERGGLAVA-----DAAARGALPADTAVALELKELTGADYEGV----S 286
            M G         E G  A+A     DAAA GA+           +  G    GV     
Sbjct: 243 KMVGVTAVDHRKVEAGAEALASELSTDAAAAGAV---------FLQAEGFGRRGVLAPQD 293

Query: 287 FTVKRGEVVGLTGATSSGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCV 346
             ++RGEV GL G   SGRT +A  + G   A  G + ++G  +       ++A GIG  
Sbjct: 294 LQLRRGEVFGLCGLLGSGRTEMARLLFGADRADCGQLRIEGKEVRLNVPRDAIAAGIGFC 353

Query: 347 PKDRHHEGLVLTQSVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVV 406
            +DR  EG +L  SV EN  + +    G F +    ++N      +  LGI     E  +
Sbjct: 354 SEDRKKEGAILELSVRENIILALQARQGLFRVLPRKRQNQIAADYVKWLGIKTADLETPI 413

Query: 407 SGLSGGNQQKVVMARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSG 466
             LSGGNQQK ++AR LAT+P +L+L +PT G+DV++K+ ++  V  +  +G ++L +S 
Sbjct: 414 GLLSGGNQQKALLARWLATDPGMLILDEPTRGIDVRAKQEIMDFVIAMCRKGMSILFISS 473

Query: 467 ELDD-LRTCDRVLVMFRGRVAAEFPAGWQDHDLIASV 502
           E+ + LR  DR+LV+   R   E+  G  D   +  V
Sbjct: 474 EIPEVLRCSDRMLVLRDRRACGEYRRGELDEQSVLQV 510



 Score = 69.3 bits (168), Expect = 3e-16
 Identities = 64/252 (25%), Positives = 112/252 (44%), Gaps = 9/252 (3%)

Query: 6   SELTSSVPVVEALEV-TKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLR 64
           SEL++      A+ +  + FG    L    +++  GE   L G  G+G++ +  +L G  
Sbjct: 264 SELSTDAAAAGAVFLQAEGFGRRGVLAPQDLQLRRGEVFGLCGLLGSGRTEMARLLFGAD 323

Query: 65  KPDTGEVRFSGAAAPSIADRDAWRERVACVYQHST---IIRDLSVAENLFINRQPLRGGV 121
           + D G++R  G        RDA    +    +       I +LSV EN+ +  Q  R G+
Sbjct: 324 RADCGQLRIEGKEVRLNVPRDAIAAGIGFCSEDRKKEGAILELSVRENIILALQA-RQGL 382

Query: 122 IDWQAMRRDARALLDHWK-IDVRE---DARAGDLSVEARQLVEIARALSYGARFIILDEP 177
                 +R  +   D+ K + ++    +   G LS   +Q   +AR L+     +ILDEP
Sbjct: 383 FRVLPRKRQNQIAADYVKWLGIKTADLETPIGLLSGGNQQKALLARWLATDPGMLILDEP 442

Query: 178 TAQLDGDEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSAL 237
           T  +D    + +   +  + R+G++ LFIS  + EV      + VLRD R         L
Sbjct: 443 TRGIDVRAKQEIMDFVIAMCRKGMSILFISSEIPEVLRCSDRMLVLRDRRACGEYRRGEL 502

Query: 238 PREQLIEAMTGE 249
             + +++ + GE
Sbjct: 503 DEQSVLQVIAGE 514


Lambda     K      H
   0.318    0.134    0.377 

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: 574
Number of extensions: 25
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 510
Length of database: 516
Length adjustment: 35
Effective length of query: 475
Effective length of database: 481
Effective search space:   228475
Effective search space used:   228475
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)

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

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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