Alignments for a candidate for rbsA in Alkalihalobacterium alkalinitrilicum DSM 22532

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= TCDB::Q9X051
         (523 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  323 bits (828), Expect = 9e-93
 Identities = 184/494 (37%), Positives = 290/494 (58%), Gaps = 4/494 (0%)

Query: 12  LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFL 71
           ++E ++I K FPG++A +NVTLQ+ +GE+ AL+GENGAGKSTLM +L G+Y   +G+I +
Sbjct: 4   VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63

Query: 72  EGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQAS 131
           +GK V+  +P  A   GI ++ Q   LV   +  ENI L +EP    G I  +K  +   
Sbjct: 64  KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAG-GKINIKKAAKAVE 122

Query: 132 KLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNI 191
            +  + G+ +DP  K++D+S   QQ V I K L   A+I+I DEPT+A+  +E  +L  I
Sbjct: 123 TISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQI 182

Query: 192 IRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRSID 251
           ++ L +EGKS+I I+H+L+EI E+ DR  V+R GR +G   I E   D L  +MVGR ++
Sbjct: 183 MKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVN 242

Query: 252 QFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTELLE 311
               K+ A   D + +++ + +    R    V+D+   V  GE+LG+ G+ G G+TEL+E
Sbjct: 243 FSVEKDPAQPKDAVLQIKDLVVKD-SRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIE 301

Query: 312 AIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITLPS 371
           AI G     T G + + G++I   +PR     G+G +P+DR   GL+L  +V  NI L +
Sbjct: 302 AITGLRK-PTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQT 360

Query: 372 VVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIK 431
              K       L  +++ K+     IE  +++TPS + +   LSGGNQQK ++A+ +   
Sbjct: 361 YYQKPYSTSGVLNFNEIYKK-ANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRS 419

Query: 432 PKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVMSEGRK 491
           P +L+  +PTRG+DV A   I+  + +    G  V+++S EL E+L +SDRI V+ EG+ 
Sbjct: 420 PDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKI 479

Query: 492 TAEFLREEVTEEDL 505
            A    ++  E +L
Sbjct: 480 VAIVDADKTNENEL 493



 Score =  100 bits (248), Expect = 2e-25
 Identities = 63/249 (25%), Positives = 133/249 (53%), Gaps = 8/249 (3%)

Query: 9   REVLLEARN-ITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEG 67
           ++ +L+ ++ + K    + AVN++ L+++ GE+  + G +G G++ L++ + G+     G
Sbjct: 253 KDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGG 312

Query: 68  QIFLEGKEVRFRNPREAQENGIALIPQELD---LVPNLSSAENIFLS---REPVNEFGVI 121
            I L G+++    PR+    G+  IPQ+     LV + +  ENI L    ++P +  GV+
Sbjct: 313 NIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVL 372

Query: 122 EYQKMFEQASKLFSKLGVNIDPK-TKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAI 180
            + +++++A++L     V    + T    LS   QQ   IA+ +     ++I  +PT  +
Sbjct: 373 NFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGL 432

Query: 181 GKRETEQLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDK 240
                E + + +   +++GK+V+ IS  L+E+  ++DR+ V+ +G+ V     ++ + ++
Sbjct: 433 DVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENE 492

Query: 241 LVRLMVGRS 249
           L  LM G S
Sbjct: 493 LGLLMAGGS 501



 Score = 92.4 bits (228), Expect = 3e-23
 Identities = 61/234 (26%), Positives = 118/234 (50%), Gaps = 16/234 (6%)

Query: 284 DDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKN 343
           D+V+  V++GE+  + G  GAG++ L+  +FG +    +G++ + GK +KI  P  A + 
Sbjct: 21  DNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPE-KGEILVKGKPVKITDPNVANRL 79

Query: 344 GIGLVPEDRKTAGLILQMSVLHNITL---PSVVMKLIVRKFGLIDSQLEKEIVRSFIEKL 400
           GIG+V +      L+ + +V  NI L   P+   K+ ++K       + K+   +     
Sbjct: 80  GIGMVHQHFM---LVEKFTVTENIILGKEPTAGGKINIKKAAKAVETISKQYGLAV---- 132

Query: 401 NIKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMA 460
                 PY  ++++S G QQ+V + K L    ++L+ DEPT  +     +E+ +++ ++ 
Sbjct: 133 -----DPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIMKKLV 187

Query: 461 VSGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSV 514
             G  +++++ +L EI+ + DR  V+  GR        E T + L    + R V
Sbjct: 188 SEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREV 241


Lambda     K      H
   0.317    0.137    0.372 

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: 643
Number of extensions: 37
Number of successful extensions: 12
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: 523
Length of database: 509
Length adjustment: 35
Effective length of query: 488
Effective length of database: 474
Effective search space:   231312
Effective search space used:   231312
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 (21.6 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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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