Alignments for a candidate for nupA in Rhizobium leguminosarum bv. trifolii WSM1325

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Rhizobium leguminosarum bv. trifolii WSM1325

Align RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate WP_012757417.1 RLEG_RS09415 ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_000023185.1:WP_012757417.1
          Length = 522

 Score =  342 bits (876), Expect = 3e-98
 Identities = 195/501 (38%), Positives = 296/501 (59%), Gaps = 9/501 (1%)

Query: 5   VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64
           ++ ++++TK F  F A + I+LD+  GEIHALLGENGAGKSTL+ ML G+LEPT G I  
Sbjct: 12  LLSVQKLTKFFGGFAACNEIDLDIAPGEIHALLGENGAGKSTLVKMLFGVLEPTGGHILW 71

Query: 65  NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKA 124
            G  V I SP ++ +LGIGMV QHF L EA TV ENI L  +      + + K  +E +A
Sbjct: 72  QGQPVAIASPGEARKLGIGMVFQHFSLFEALTVAENIALSLD----DAIPIDKIAEEARA 127

Query: 125 LSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIM 184
           LS  YGL +DP+A +AD+SVG +QR+EI++ L +   ++I DEPT+VLTP E   L   +
Sbjct: 128 LSIAYGLPLDPHAHVADLSVGERQRIEIVRALLQNPKLIILDEPTSVLTPQEADRLFETL 187

Query: 185 KSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSVSF 244
             L  EG+S++ I+H+L+E++ + DR TV+R G+     +    T   LA MMVG  V+ 
Sbjct: 188 FKLRAEGRSVLYISHRLEEVQRICDRATVLRHGRVTGACDPKHETPASLARMMVGSEVAT 247

Query: 245 TIEKTPTKPKETILSIKDLVVNENRGIP-AIKGLSLEVKAGEIIGIAGIDGNGQSELVQA 303
                 +   E  L++ +L V         ++ +S+ V++GEI+ IAG+ GNGQSEL  A
Sbjct: 248 VTHPERSDKGEIQLAVANLSVAARTPFAMPLRDVSMAVRSGEILAIAGVAGNGQSELFDA 307

Query: 304 ITGLRKIKSGH-LTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLAL--- 359
           ++G   + S   + I+ + V          L  G VPE+RH    +  + +++NL L   
Sbjct: 308 LSGEYPVVSAEAIVIRKRPVGNQGITARRLLGAGFVPEERHGHAAVSAMKLSDNLVLARS 367

Query: 360 QTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDR 419
           Q+  KA L   G++ ++ +    R + +  DVR +++   A   SGGN QK I+ RE+DR
Sbjct: 368 QSDRKAFLGLLGIIRHAAVKSAARRISEAMDVRKSSDDPAAGSLSGGNLQKFIVGRELDR 427

Query: 420 DPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQ 479
            P +L+V+QPT G+D GA   I + L+     G AV+++S +LDEI  ++  IAVI +G+
Sbjct: 428 QPAVLVVNQPTWGVDAGAASRIRQALVDLARAGSAVVVISQDLDEIFEVATDIAVICEGR 487

Query: 480 IQGIVTPETTNKQELGILMAG 500
           +          ++ +G+LM G
Sbjct: 488 LSRPFPAGELTRERIGLLMGG 508



 Score = 89.0 bits (219), Expect = 4e-22
 Identities = 65/234 (27%), Positives = 110/234 (47%), Gaps = 12/234 (5%)

Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329
           G  A   + L++  GEI  + G +G G+S LV+ + G+ +   GH+  +GQ V   S  +
Sbjct: 24  GFAACNEIDLDIAPGEIHALLGENGAGKSTLVKMLFGVLEPTGGHILWQGQPVAIASPGE 83

Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEF 389
             +L +G V +      L   LT+AEN+AL      P+         KI E  R L   +
Sbjct: 84  ARKLGIGMVFQ---HFSLFEALTVAENIALSLDDAIPID--------KIAEEARALSIAY 132

Query: 390 DVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAER 449
            +   +        S G +Q+  I R + ++P L+I+ +PT  L     + + + L   R
Sbjct: 133 GLP-LDPHAHVADLSVGERQRIEIVRALLQNPKLIILDEPTSVLTPQEADRLFETLFKLR 191

Query: 450 DEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGGSI 503
            EG++VL +S  L+E+  + DR  V+  G++ G   P+      L  +M G  +
Sbjct: 192 AEGRSVLYISHRLEEVQRICDRATVLRHGRVTGACDPKHETPASLARMMVGSEV 245



 Score = 57.4 bits (137), Expect = 1e-12
 Identities = 59/242 (24%), Positives = 103/242 (42%), Gaps = 18/242 (7%)

Query: 24  INLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSG-SIKINGSAVTIDSPSKSAQLGI 82
           +++ +R GEI A+ G  G G+S L + L+G     S  +I I    V     +    LG 
Sbjct: 281 VSMAVRSGEILAIAGVAGNGQSELFDALSGEYPVVSAEAIVIRKRPVGNQGITARRLLGA 340

Query: 83  GMV----HQHFMLVEAFTVTENIILGNEVVKN----GILDL------KKAGQEIKALSEK 128
           G V    H H   V A  +++N++L           G+L +      K A + I    + 
Sbjct: 341 GFVPEERHGH-AAVSAMKLSDNLVLARSQSDRKAFLGLLGIIRHAAVKSAARRISEAMDV 399

Query: 129 YGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMKSLV 188
              + DP A    +S G  Q+  + + L R   +L+ ++PT  +       +   +  L 
Sbjct: 400 RKSSDDPAA--GSLSGGNLQKFIVGRELDRQPAVLVVNQPTWGVDAGAASRIRQALVDLA 457

Query: 189 KEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSVSFTIEK 248
           + G ++++I+  LDEI  VA  + VI  G+          T + +  +M G   S +  +
Sbjct: 458 RAGSAVVVISQDLDEIFEVATDIAVICEGRLSRPFPAGELTRERIGLLMGGLHESSSPPE 517

Query: 249 TP 250
            P
Sbjct: 518 AP 519


Lambda     K      H
   0.315    0.135    0.363 

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: 559
Number of extensions: 23
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 510
Length of database: 522
Length adjustment: 35
Effective length of query: 475
Effective length of database: 487
Effective search space:   231325
Effective search space used:   231325
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: 42 (22.0 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update 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