Alignments for a candidate for HSERO_RS03640 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Herbaspirillum seropedicae SmR1

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate HSERO_RS05320 HSERO_RS05320 ribonucleotide-diphosphate reductase subunit alpha

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__HerbieS:HSERO_RS05320
          Length = 502

 Score =  409 bits (1052), Expect = e-118
 Identities = 222/503 (44%), Positives = 312/503 (62%), Gaps = 3/503 (0%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           +LQ+ GI+K+FG    L  + L +R GE+HAL+GENGAGKSTLMK+L G+  PD GEI +
Sbjct: 1   MLQLTGIKKNFGPVTVLRGVDLEVRAGEVHALLGENGAGKSTLMKILCGIVRPDAGEIRI 60

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125
           DG+P       A+ A G+ +++QE ++ P +    N+F+  ELR+R G +  AAMR R  
Sbjct: 61  DGQPCRFDSYRAAIAGGVGVVFQEFSLIPYLDAVDNMFLARELRSRWGWLQRAAMRRRAQ 120

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
            ++ QLG          +LS+A+QQ VEIA+AL   +RI+++DEPTA L+  E E LF V
Sbjct: 121 EIIGQLGVAIPLDVPVCKLSVAQQQFVEIAKALALDARILVLDEPTATLTPAEVEHLFAV 180

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           +R LR +G+AII+ISH + E++ + DR+TVLRDG++V      E+D  R+V+MMVGR + 
Sbjct: 181 MRSLRAQGVAIIFISHHLEEIFEICDRITVLRDGAYVATCATAEVDQARLVEMMVGRRIE 240

Query: 246 EFYQHQRIAPADAAQLPTVMQVRALAGGKIRPAS-FDVRAGEVLGFAGLVGAGRTELARL 304
             +   + A     +   V++V AL   +  P S F +R GE+LGFAGLVG+GRTE    
Sbjct: 241 NCFP-PKPAKGGEGEGEVVLEVHALQLRRQAPVSQFQLRRGEILGFAGLVGSGRTETVLA 299

Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364
           + GA       + + G P+    P  A++AGI  +PE RK QGL    ++  N ++N   
Sbjct: 300 MLGAHAALSCKLSMHGVPLRFADPAQALQAGIGLLPESRKEQGLITSFSILHNVSLNNYG 359

Query: 365 RHTRLGLVRSRSLGGVA-RAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423
           ++   GL   R     A  AA+QR+ VK    +  V  LSGGNQQKV++ARW+  A KVL
Sbjct: 360 KYRLGGLFLDRRREQQATEAAMQRVRVKAPGAQVRVDTLSGGNQQKVVIARWINHAMKVL 419

Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 483
           I DEPTRG+D+ AKSEIYQL+    +QG ++++ISSELPEV+G+ DRV V R G I   L
Sbjct: 420 IFDEPTRGIDVGAKSEIYQLMREFTAQGYSILMISSELPEVVGMADRVCVFRGGGIVATL 479

Query: 484 AGAAITQENIMRLATDTNVPRTA 506
            G A+  E IM  AT   +   A
Sbjct: 480 EGEAVNAEEIMTHATTGRIRHAA 502



 Score =  105 bits (261), Expect = 5e-27
 Identities = 67/233 (28%), Positives = 115/233 (49%), Gaps = 5/233 (2%)

Query: 275 IRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRA 334
           +R    +VRAGEV    G  GAG++ L ++L G      G+I ++G+P   D  RAA+  
Sbjct: 17  LRGVDLEVRAGEVHALLGENGAGKSTLMKILCGIVRPDAGEIRIDGQPCRFDSYRAAIAG 76

Query: 335 GIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAH 394
           G+  V ++       +    A +         +R G ++  ++   A+  I +L V +  
Sbjct: 77  GVGVVFQEFS----LIPYLDAVDNMFLARELRSRWGWLQRAAMRRRAQEIIGQLGVAIPL 132

Query: 395 PETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAV 454
            + PV KLS   QQ V +A+ L +  ++L+LDEPT  +       ++ ++  L +QGVA+
Sbjct: 133 -DVPVCKLSVAQQQFVEIAKALALDARILVLDEPTATLTPAEVEHLFAVMRSLRAQGVAI 191

Query: 455 VVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAP 507
           + IS  L E+  ICDR+ V+R+G      A A + Q  ++ +     +    P
Sbjct: 192 IFISHHLEEIFEICDRITVLRDGAYVATCATAEVDQARLVEMMVGRRIENCFP 244


Lambda     K      H
   0.320    0.135    0.378 

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: 723
Number of extensions: 31
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: 521
Length of database: 502
Length adjustment: 35
Effective length of query: 486
Effective length of database: 467
Effective search space:   226962
Effective search space used:   226962
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.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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