Alignments for a candidate for HSERO_RS03640 in Beijerinckia indica ATCC 9039

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Beijerinckia indica ATCC 9039

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_012386370.1 BIND_RS17610 ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_000019845.1:WP_012386370.1
          Length = 548

 Score =  159 bits (403), Expect = 2e-43
 Identities = 159/516 (30%), Positives = 248/516 (48%), Gaps = 53/516 (10%)

Query: 2   TQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKS-TLMKVLSGVHAPDQ 60
           T  PLL  R +  S+G    + D+ L++ PGE  AL+GE+G+GKS T +  L  +  P +
Sbjct: 14  TDKPLLAFRDLSISYGGQAIVRDLTLSLHPGETAALVGESGSGKSQTALAALRLLPEPAK 73

Query: 61  --GEILLDGRPV-ALRDPGASRAAG--INLIYQE--LAVAPNISVAANVFMGSELRTRLG 113
             G+IL +G+ + +L +   +R  G  I LI+QE   A+ P   V A +  G  LR  LG
Sbjct: 74  VSGQILFEGQDLLSLSELALNRLRGRRIALIFQEPMSALDPLFPVGAQI--GVILRHHLG 131

Query: 114 LIDHAAMRSRTDAVLRQLGAGFGASDLAG---RLSIAEQQQVEIARALVHRSRIVIMDEP 170
           L   AA+ +R   +L Q+G       +      LS  ++Q+V IA A+     ++I DEP
Sbjct: 132 LSRRAAL-TRACELLDQVGIPDPQRRVKAYPHELSGGQRQRVAIAMAIACEPAVLIADEP 190

Query: 171 TAALSERETEQLFNVVRRLRDE-GLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDE 229
           T AL      ++ +++  L+   G+A+++ISH +  V  +AD V V+  G  V      E
Sbjct: 191 TTALDVTLAARILDLIEDLKQRLGMALLFISHDLGLVRRIADSVHVMHQGRIVESGPARE 250

Query: 230 I---DSERIVQMMVGRSLSEFYQHQRIAP--------ADAAQLPTVMQVRALAG----GK 274
           I     E   ++++G +        R+ P         +A  L    + R   G    G 
Sbjct: 251 IIHHPREAYTRLLLGAA-----PRPRLRPHPLEAKNLLEARDLTVRFKRRGTLGLPSFGL 305

Query: 275 IRPASFD----------VRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVH 324
            RP   D          +R GE  G  G  G+G++ LAR L    P SG  IL EGR + 
Sbjct: 306 FRPREKDFTAVDHVNLTLRQGETFGLVGESGSGKSTLARALLRLVPASGS-ILFEGRDLV 364

Query: 325 IDQPRAA--MRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVAR 382
             QPRA    R  +  V +D   Q L  +M + A  T  +      L    +++L   A 
Sbjct: 365 ALQPRALRPFRHAMQIVFQDPY-QALSPRMRIGAIITEGLRIHEPGLN---AQALDARAA 420

Query: 383 AAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQ 442
            A+Q + +  A       + SGG +Q++ +AR + + PK+L+LDEPT  +D   ++EI +
Sbjct: 421 FALQEVKLDPALRHRFPAECSGGQRQRIAIARAMILRPKLLLLDEPTSALDRSVQAEILE 480

Query: 443 LVHRL-ASQGVAVVVISSELPEVIGICDRVLVMREG 477
           L+  L AS G+  + IS +   V  + D + VMR G
Sbjct: 481 LLSLLQASHGLTYLFISHDFGAVRAMADTIGVMRMG 516



 Score = 89.7 bits (221), Expect = 2e-22
 Identities = 64/216 (29%), Positives = 115/216 (53%), Gaps = 9/216 (4%)

Query: 21  ALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRA 80
           A+  ++LT+R GE   L+GE+G+GKSTL + L  +  P  G IL +GR +    P A R 
Sbjct: 315 AVDHVNLTLRQGETFGLVGESGSGKSTLARALLRL-VPASGSILFEGRDLVALQPRALRP 373

Query: 81  A--GINLIYQE--LAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDAVLRQLGAGFG 136
               + +++Q+   A++P + + A +  G  LR     ++  A+ +R    L+++     
Sbjct: 374 FRHAMQIVFQDPYQALSPRMRIGAIITEG--LRIHEPGLNAQALDARAAFALQEVKLDPA 431

Query: 137 ASD-LAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLR-DEGL 194
                    S  ++Q++ IARA++ R +++++DEPT+AL      ++  ++  L+   GL
Sbjct: 432 LRHRFPAECSGGQRQRIAIARAMILRPKLLLLDEPTSALDRSVQAEILELLSLLQASHGL 491

Query: 195 AIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEI 230
             ++ISH    V A+AD + V+R G  V     +EI
Sbjct: 492 TYLFISHDFGAVRAMADTIGVMRMGHLVESGPAEEI 527


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: 674
Number of extensions: 41
Number of successful extensions: 9
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: 548
Length adjustment: 35
Effective length of query: 486
Effective length of database: 513
Effective search space:   249318
Effective search space used:   249318
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 24 2021. The underlying query database was built on Sep 17 2021.

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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